FE9 is the best IMO. The story is one of, if not the best, in the series and the gameplay is really well balanced and rewarding (bonus exp).
FE3 I kind of like more than FE12. The latter is probably the better game, but the former has more charm IMO, and also more levels.
FE2 I find to be underrated.
The GBA games are good.
FE10 has great storywise, but it destroyed supports and the non-Ike levels are a tad unbalanced/annoying.
FE11 stayed too close to the original and feels like a missed opportunity in most respects. Also it's dumb you have to killl characters to unlock the new ones.
Awakening is a good game, but it's just one that I can't help but get all nit-picky about.
- The story is worst in the series (FE1 gets a pass IMO, the remakes/sequel really help as well).
- We didn't need a story for most of the DLC/probably would gave been better to keep the games in separate universes.
- It messed up in it's attempt to appeal to older fans. Seriously Marth & Grima, WTF happened after FE3?
- The lack of color (everything is too brown, and Olivia is the only non-status quo or returning character with unnatural hair).
- The character portraits don't blink or move their mouths.
- Lots of anime stereotypes.
- Chris did the whole "My Unit" thing significantly better.
- No online multiplayer.
- Questionable DLC.
- Lack of variety in missions.
- Unbalanced even for having the ability to grind like in FE2/8.
Fates seems to address a fair amount of these issues,
at least it seems, but I just can't get over the fact that Phoenix Mode exists, and just how shameless the game is (borderline hentai level content, and pay-to-unlock DLC).