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.
For me personally, it's not that the updates made the game worse, they made it better a bit I guess. They just tend to turn up disappointing compared the hype that's raised surrounding them just before the updates involved usually. I could care less about ender chests though and endermen were probably one of my favorite updates.
I'm honestly a little concerned that they'll put the block ids thing on the backburner for a while now.
What Iceball said. I don't hate the updates in the sense that my game is "RUINED FOREVER", I just hate them in the sense that they built up a lot of hype, and made it meh.
Exception is Endermen, I hated the guys back when they picked everything up, now, not so much. But they should still drop the blocks they hold.
Also, enderchests are kinda cool. It's just that they have a global inventory, so playing in a multiplayer game allows others to steal your stuff mid-trade.
Finally, the SSPSMP merge, I hate it, because all the lags and stuff are going to be applied in single player. I know that it'll be fixed in due time, however, so I only hope they do it right.