The feathers sort of served a purpose. Getting 50 of them unlocked a new Warhammer, and getting all 100 unlocked a cape that made the game a lot harder (Although truthfully, it would have been better if getting all 100 feathers unlocked the cape across all playthroughs, because by the time you've gotten through enough of the game to be able to get all the feathers, the game's mostly over already).
But I agree that the money in AC2 needed to be thought out better. It did give me a sense of satisfaction to upgrade the villa and watch it come to life due to my actions, but it served little purpose outside of that. Ubisoft promises to expand on the villa upgrade system in Brotherhood, however.
I liked the side quests in Fallout 3. While they all did have achievements hanging over them, they also had great rewards. Completing Agatha's Song fully granted you a new radio station and the Blackhawk. Doing Riley's Rangers netted you the best non-power armor in the game, plus a new safe house and some other goodies. Doing Stealing Independence got you a great ammo vender (Sydney) and the schematics to the Railway Rifle.
I suppose my point is, games can do sidequests right so that they have great rewards and stuff, but most don't, and I guess the achievements are allowing designers to get away with that a bit more easily now.