Some very useful tricks were nerfed directly: you can't draw and throw more than one alchemical item per turn (pure arbitrariness, I say); Blink doesn't let you sneak attack; trapfinding can now be done by everybody, with Perception relying on Wis, making Rogues more MAD (whereas Search in 3.5 relied on Int, which Rogues usually had in spades but few others had). There are others.
Apart from that, the relative nerf is what people get agitated about. Fewer skills means everybody gets to get a few essential ones (like Perception, s.a.), with Rogues losing their niche of 'skillmonkey' in comparison. Fighter weapon training, Barbarian rage powers etc. cut down on the comparative combat performance of Rogues.
All in all, Rogues lost niche protection and didn't gain anything in return. Most classes received significant buffs or at least gained lots of versatility, while Rogues simply lack in most areas now, where before they had some areas of expertise nobody else could duplicate.
I'm still of the opinion that you can play a very effective Rogue - AND that the class can be tons of fun. But it's got next to nothing going for it that other classes couldn't emulate, or even outright do better.