I hate the later versions not because of the ravines, the mines and pistons, but:
Villages - Paths are borked. I'm sorry if that wasn't clarified in the previous post, but yeah, the village gravel roads are almost always unaligned, requiring some work in order to make it not look like crud.
Endermen - Because they pick up blocks? Fortunately, the nerf has significantly lowered the amount of blocks they pick up. Basically, in the old versions, given enough time, endermen could totally level a chunk. Now, they can only destroy mud huts and gardens. Wouldn't be a problem, honestly if they dropped the block they were holding, which is something they don't do.
The End - It was honestly lacking, and the Enderdragon just bumped into you as a means of attack. Would be fun if it had more attacks, but right now, it's more or less a battle of attrition. Oh, and endereggs have no use.
More meta stuff:
Block IDs - Only applicable to people who install mods, but the fact that the ID limit increase is already there, but the game thinks it doesn't exist kind of sucks. Personally, I don't hate this much, but yeah, for mod players, this really limits their own choices.
Current snapshot stuff:
SSP+SMP merge - Oh come on, I don't want to play multiplayer while I singleplayer.
Enderchests - Can only contain one inventory per world, which means that in servers, you can only make 1 mega storage (by this, I mean a warehouse hub, much like a bank), and even then, someone with enderstorage could intercept your item trade to someone else. Don't mind this much, personally.
Villages - So wait, having villages makes your world WORSE? They need work but, what? The paths are weird a lot, but that doesn't mean it makes the game WORSE.
Endermen - Thats been fixed, and honestly I never had it happen to me (although I know its happened to other people).
The End - Again, it being there makes the game worse? A optional thing, that has no effect on the rest of the game, which is in essence just more content makes the game worse? whaaaaaa?
Blocks ID - That's a bug, so It'll probably be fixed.
SSP+SMP merge - We have NO idea what this means. Honestly, all we have now is speculation. Please don't freak out at speculation. IF something happens that you don't like, then say something about it (again, makes the game WORSE not just another feature which you don't have to use).
Enderchests - Again, another extra feature that you don't have to use. Its an option if you want it, and if you don't use the mod or just don't use it at all.