I really can't pick just one, so I'm just gonna point out 3 characters I hate equally.
1. Rhajat : She's a poor copy of Tharja, and I have a sneaking suspicion that the writers made her bisexual solely for the sexual appeal. I get that FE has a history with using fan service, but I still feel like that's scummy move given that LGBTQ+ characters get ruined by that kind of crap all the time. To be perfectly honest the "appeal" her character is supposed to have mostly just puts a bad taste in my mouth.
2. Lachesis : I know that Ephraim and Eirika get crap for being a little too close (which is probably over hyped anyway), but I feel like they pale in comparison to the incest baggage Lachesis is packing. Long story short, it makes me super uncomfortable, and in my opinion it almost bleeds out into having a negative effect on Edilgan's character (ALMOST).
3. Sumia: It's usually don't get angry through a feminist lens, but SWEET OL' SUMIA gets me out of my shell. I loathe how Awakening sets out on a blood mission to pair her with Chrom, then proceeds to make her an insecure, overly emotional, spoiled girl that bakes pies. Normally I wouldn't hate a character on those traits alone, the thing that really upsets me is the fact that she needs to be dependent upon others to function ( Not in a teamwork and freindship sort of way, in a "I need someone to think for me because I'm weak" kind of way).