I've been contributing to Three Houses's page on The Cutting Room Floor for quite a while, and the sheer amount of stuff I have documented in it about scrapped stuff is quite impressive honestly. Something which isn't discussed often however is what some of the stuff found there implies for the game's development, which is kind of the reason this thread was made.
Full disclosure: The info I'll speak about has been found and corroborated with people like DeathChaos and the fedatamine.com team, who have hacked and datamined the game. The only thing I've done myself is reporting the unused content they've uncovered in places like TCRF and NIWA’s Fire Emblem wiki, and analyzed the internal number of the game’s voice clips based on a rip someone did of the game’s files some time ago.
Also, while this post might be familiar to some as I already posted a previous version of it on reddit, some of the stuff here has been revised and new tidbits were added which might be of interest for some (perhaps?).
Without futher ado, let's get to the nitty gritty:
1. Thales, the sword-wielding priest???
In the game’s files there’s an unused agarthan sword called Ridill, whose description flat out states it was meant to be Thales’s signature weapon before Quake Σ took it’s place. While it’s currently unknown if the weapon has a unique model (or if it works at all), it’s interesting to note the description calls Thales a priest, rather than a guru as his class’s description does.
I checked the japanese script to see if the sword’s english description happened to be a mistranslation, and it turns out that is not the case! In japanese, the characters used are “祭司“, which can be literally translated as "priest" or "seer". By contrast, Thales’s Agastya class calls him a “導師”, which more or less means “a sage/mage/guru with high authority”, thus it can be translated in far more ways than simply "priest".
So yeah, this bit is quite tame overall given it’s mostly about semantics.
2. Cleobulus, the missing(?) agarthan.
In the character data, between the generic TWSITD members found in Silver Snow/Verdant Wind’s Shambhala chapter lies an unused minor character boss who goes by the name of Cleobulus. The presence of this scrapped character is intriguing for 2 main reasons:
a) Sans Kronya and Odesse, most of the important agarthan members are named after the Seven Sages of Greece, and in the base game there just so happens that there’s seemingly no seventh member to be seen...
b) There is also an important agarthan member whose true identity is never revealed in the game: Cornelia, the court mage of Faerghus. While the character data displays the unused agarthan as a male (normally debunking whatever theory one could make about this), I also noticed one of the generic named slitherers (Bias) happens to be internally set a male Holy Knight when in-game they're a Gremory (which is female-locked). So I went and asked DeathChaos some time ago what was up with that, and here's the response I got:
3. Quests would have unlocked everything, even scrapped features.
There is an insane amount of unused quests, and a bunch of them were meant for features which are either already available by default, were changed in the game or are simply scrapped. Want to tutor a student? You had to do a quest first. Exchange travelers? Hear the game’s soundtrack in Manuela’s office? Allow your students to do Certification Exams? Repair weapons? You know the drill, and this also applies for scrapped features like riding horses, trading items + getting books through it, unlocking new personal info about your students, etc.
4. Some characters have doppelgänger problems.
Besides the already existing variations some characters have for story purposes like !Child Edelgard & Dimitri, there's also a few duplicates of some characters running around which most players have likely already spotted without realizing it:
a) The Gilbert that aids you in Chapter 5 is a completely different character from the one you get in Azure Moon. This incidentally explains why he so happens to lack his personal ability during that map.
d) The Flame Emperor seen in Chapter 6 is different to the one the game uses for story scenes and Chapter 11 in BL/GD. She seems to exist only so her name can be seen as ??? in the game's dialogue during battle. By contrast, the in-game event engine manually changes the name of the other Emperor to ??? during story scenes.
c) Chapter 12 for some odd reason uses a completely different Edelgard compared to the one that's playable. While I'm not exactly sure why that's the case, I did notice that the stats she boasts in that mission are barely any higher compared to the previous chapter...
d) Lastly, both the masked and playable Jeritza added via DLC are internally considered their own separate entity. The former has barely any data to speak of and doesn't even have a personal skill, though interestingly, he does bear a Minor Crest of Lamine similar to his playable self.
5. Many story scenarios and set pieces were likely planned in advance, way before their triggers were even implemented.
The internal order of story events and the voice clips surrounding them are fascinating to analyze, as it might shred light on the how some stuff was implemented into the game plus the time it was implemented into development. For example:
Ever wondered why the Blue Lions and Golden Deer routes get a scene prior to the Holy Tomb event with the Flame Emperor reveal which the Black Eagles don't have? Well, internally, Edelgard's coronation is located right next to those events, which suggests her scene is meant to serve as a counterpart of sorts.
Caspar and Linhardt's lines as enemies on the event prior to the Fort Merceus mission from Verdant Wind actually originate from the Silver Snow route, as not only that version of the event comes first internally, the voice clips used are also located in the area where their Church route story clips are located. This also happens to double as leftovers of a scrapped feature Silver Snow had at one point where the Black Eagles who fell in Part 1 of Classic Mode showed up in Part 2 as enemies later (the devs didn't do a good job at scrubbing it, truth be told).
Dedue’s return in Azure Moon was planned way before his paralogue was made, and that includes Felix & Annette’s scrapped defection as their clips are located in the area of their Blue Lion story clips lie.
Lorenz’s scrapped defection on Verdant Wind has his battle clips against Claude in both the Azure Moon and Verdant Wind’s version of Chapter 16, while the monastery exploration clips where the Hilda, Raphael and Marianne acknowledge his demise exist only for Verdant Wind.
Of course, this also begs the question: what scenarios were added late in development then? The short answer is: everything related to paralogues, including the Death Knight/Jeritza’s unlockable death scene in Azure Moon, as the location of its voice clips suggests it was added right after their paralogue was finished (AKA way after Azure Moon was finished). This incidentally also corroborates what a previous developer interview said about Mercedes:
6. Gronder Field 2? In my Silver Snow? It’s more likely than you think.
Anyone who has played the Silver Snow route knows that its story conveniently skips the Gronder Field 2 battle and the whole month in which happens because of reasons. In spite of this, there is actual circumstantial evidence pointing the devs briefly considered giving said route their own version of that chapter:
a) One of the two unused maps in the game is set to load Gronder Field 2 as the battleground, is internally called as a Chapter 17 of some undefined route, and only contains enemy and deployment placeholders only for the Black Eagles slot, while the other 2 slots for Azure Moon and Verdant Wind are empty (in case anyone wonders, both Silver Snow and Crimson Flower share the same slot internally when loading a specific map, meaning it’s entirely possible though hacking to load any map from SS into CF and make it work with mostly no issues).
b) A specific map having data for only one route is a quirk which only exist for route-exclusive missions like the ones from Crimson Flower and Azure Moon, while everything else which is shared between 2 or more routes (like most of part 1 & 2 + the chapters shared between the Church and Claude’s routes) have data filled in their 2/3 slots respectively.
c) In the monastery exploration script, there is one empty slot between the Silver Snow and Azure Moon routes. Had a proper Chapter 17 been added into into SS, the only data which would’ve needed to be repointed to preserve a consistent internal order would’ve been only the stuff concerning Silver Snow’s exploration.
d) There is an awkward difficulty spike between Silver Snow’s Chapter 16 and 17 where the enemy’s levels go up by 4 instead of 2. This issue doesn’t exist in Azure Moon and Verdant Wind as the Gronder Field 2 battle makes sure the transition between each chapter is slightly more smooth stat-wise.
e) 10 Placeholder event slots exist between the story and paralogue stuff, so adding more story scenes to Silver Snow without messing up anything afterwards would've been possible (there are also 16 more placeholders between the paralogues and Cindered Shadows, but I don't know if those existed prior to the release of the DLC).
7. "Wait, one of the two unused maps? What’s the other one about?"
The second unused map has the same enemy and deployment data as the first one, with the difference it loads Fort Merceus as a battle location and it internally calls itself as a Chapter 18 of a non-defined route.
Unfortunately, there’s very little evidence suggesting plans for that one. If I had to make a guess though, I dare say the Fort Merceus infiltrations for Silver Snow and Verdant Wind were planned to be far more distinct at first before both maps where combined into one spot. This is 100% conjecture from my part though, so there’s a good chance I might be wrong.
8. "What about Crimson Flower? Could have Gronder 2 or Fort Merceus been planned for that route?"
Location wise, the battle script of the Crimson Flower's maps (Chapter 12-17) is all gathered together after Verdant Wind and before the paralogues. Meanwhile, CF's exploration script comes after Part 1 but before Silver Snow, Azure Moon and Verdant Wind's, so overall I find very unlikely those unused maps could have been planned for Edelgard's route.
9. Crimson Flower was likely saved for last (before the paralogues) and thus rushed, NOT unfinished.
Before getting into this, I think it's important to clarify the distinction between the words rushed and unfinished, as they have different implications in spite of being used interchangeably by many. Rushed means some action/object was made hastily and under a low interval of time. Unfinished meanwhile, more or less indicates some action, product or something was never finished or given any conclusion of sorts.
With that out of the way, let's talk about the 2 points which suggests Crimson Flower fits the former description rather than the latter.
a) Scrapped class sprites of Rhea and Dimitri sporting their unique appearances in CF is the only thing left unused for that route on launch, and Jeritza as a whole was more or less left as a huge blank both story and data wise before the post launch updates happened. By contrast, the other 3 routes have quite the amount of unused story, battle dialogue and scrapped defection situations.
b) While most story events are internally listed in chronological order for Silver Snow, Azure Moon and Verdant Wind (sort of, it kinda jumps at the middle of each one before wrapping them up later), Crimson Flower instead has its own not only listed after all three, but also has its very last event listed in the data be the scene in which Rhea attacks Byleth and kickstarts the time skip. I think it goes without saying what this implies given how the route's well known at this point for lacking animated cutscenes besides the ending.
Before wrapping up, here are some honorable mentions I didn't consider huge enough to deserve their own spotlight:
Scrapped dialogue & voiceclips suggest Silver Snow's Endgame was even harder at one point, as they point out the player would have needed to seize 3 separate reinforcement spots rather than just 1 to stop the White Beasts from spawning.
The enemy Death Knight class is capable of teaching a playable unit the Heartseeker skill once mastered. This is the only case where an enemy only class can do so, as not even the Flame Emperor class (which is a palette/model swap of Edelgard's Armored Lord class) can do it.
Speaking of Death Knight, after the Wave 3 update, data was added in CF's Chapter 12's exploration to make Jeritza/Emile appear in it to say hi and confirm he's the Death Knight earlier, which was dummied out.
Regarding the unused maps mentioned earlier, those happen to be the only ones which deliberately call for Female Byleth in the deployment slots (by comparison, the game runs a code to swap Male Byleth for the Female one if it checks she was chosen at the start of the game in the other maps). Given that some cutscene stuff suggest !FByteth was added later in development, there's a huge chance the devs used those maps to test her out.
So…yeah. If I had to describe this game's development with a few words, I dare say Intelligent Systems and Koei Tecmo tried to bite far, far more than they could chew with this one. I mean, it's well known the game was delayed twice so...
(Also there's still far more unused stuff I didn't cover here. The iceberg goes deep folks!)