I feel like they should just bring back the magic triangle. Best as i could really tell there were no limits on the Nosferatu tomes so you ended up with really overpowered mages, plus i ended up just relying on Nyx for all my magical needs and used Elise for healing mostly. Also i like what they did with the mu being the main character but he should have been less perfect(and yes i know others have voiced this same opinion but that doesn't make it any less true.)
I also feel they nerfed the spear WAY too much. at this point its hardly worth using. The lack of weapon durability was a plus as far as i'm concerned, its so annoying to have to send money on new weapons every other map and made me rely mostly on one or two units in previous games in order to combat that.
There was also no reason to really rush through the conquest maps (don't know if this is true for the other two games) so i basically turtled my way through most of the maps. There also weren't many high crit units until you got the killer weapons. I remember playing sacred stone and binding blade and having mymridons ( especially Joshua) with exceptionally high crit rates.
I won't say much on the story since its already been thoroughly discussed. On the subject of children and marriages however i feel like they should have a post main story line where the children show up and they age the main characters by a few years, or give you a whole new team, but thats just my opinion and i a m open to criticism. Also the whole hero worship for the MU. I know i said i wouldn't address this but i have to. It was alright for the first few chapters but by the Izana chapter it should have disappeared. except maybe for the side you chose.
I hate how they looped Valla into conquest, i basically had to ignore it whenever they mentioned it to avoid putting my foot through the screen. enough said.