I personally think the liberties taken upon Awakening's story were due to a lack of budget, rather than a lack of good ideas. The game's story had a lot of potential to be much better, sure, but the game might have been the last we ever got, and IntSys scrapped together all their funds for this one.
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From the very beginning of the game, you are thrown into your "Final Battle", and kill Chrom. You have no real reason why your Avatar would do this, you know nothing of his or her motives, where you have been placed or what's even going on. Then you're awoken by the very same man you just killed. The Chapter's name sets it up quite well, it's not something that's happened, it's a Premonition. At some point you know you will backstab this man, whoever he is, and wind up killing him. From the literal start of the game, you have two giant threats looming over your head as you slowly grow more attached to the cast, the bleak future that is to come, and the fact you kill Chrom, for whatever reason.
After that literal ton of foreshadowing, the game takes a more natural Fire Emblem approach, there's a nation, Plegia, troubling yours. And a common enemy, the Risen. Whether Plegia is having trouble with the Risen is never stated, but I like to assume they spread all over the world as they first appear with the Children. Assumingly, those Gates (like what Lucina jumps out of) appeared all over the World as the 16 Children came back. This would explain how they got scattered, too.
Gangrel is probably the best villain in the game, despite my huge bias to WARE WA GURIMREI, as he's one of those villains who you are made to hate. First with his capture of Maribelle, then with the murder of Emmeryn, and just the way he taunts you all the way up to Chapter 11 before you finally get to kill him.
Grima is actually one of my favourite villains in the series because s/he is so mysterious. He introduces himself to the player in Chapter 6, with the very same character who you killed in the Premonition. Further amplifying connections between the two when it happens again, I believe this is after Chapter 10? I like how the threat of Grima is presented to the player, this unstoppable god of destruction being revived and wiping out the world, yet s/he has been with you the entire time. And in essence, you ARE Grima. I mean, I look at it this way. Robin is the Avatar of Grima, and Chrom is the Avatar of Naga. They both to a degree symbolise the dragons they represent, Robin through Cunning, Guile and Betrayal, and Chrom through Caring and Companionship.
Walhart, while he is my least favourite of the 3, mostly from coming at a massive low point in the game's story, is actually a great villain because he has similar ideals to Emmeryn. Different methods of course, but outside of Grima, none of the 3 main villains are really heartless monsters, they all have reasons for their actions and once you can get behind them they make a lot more sense as characters.
Overall, Awakening's major problem was it's story. The gameplay was for the most part top notch and thankfully a lot of the budget went to that it seems. Liberties had to be taken somewhere and it unfortunately happened in the characters. While I personally don't find any of the characters that "flat" or 1 dimensional, that may be because of my personal bias towards them. I can certainly see the flaws with Awakening, but I love it all the same for it's much improved game system, and the characters who are good are really good. I personally don't think that while a game should be striving for deep characters, it's really that necessary. I am thankful that the budget went to the gameplay, and not making Olivia have more traits that make her best girl. (Because I mean, come on) I think that Awakening's character quirks add a whole lot of depth to them, it just requires viewing a lot of the support conversations and realising the characters at time can be a bit rigid due to lack of development funds.