Uncharted 2 is held in very high regards, perhaps too high. It was innovative when it came out, but Uncharted 3 is the better game. Here's why:

Uncharted 3 Pros:

Better set pieces:  The burning Chateau and catching a flight alone blow away any set piece in Uncharted 2.

Better story: Uncharted 2's story was predictable from beginning to end while 3 has some nice plot twists that keep the story engaging though you know where it will ultimately go.

Better melee: Both games have sluggish melee with no depth but Uncharted 3's melee atleast is visually satisfying.

More variety in combat: Uncharted 3 has all the variety of Uncharted 2 and then some. You can shoot while swimming that adds a lot to the combat in some of the chapters.

Better encounters: Both games have great encounters but Uncharted 3 has better ones. The difference isn't that big though. The shipyard encounter especially allowed for some very diverse tactics and the following ewncounters in the shipwreck and one the boat were some of the highlights.

Better puzzles: Uncharted 3's puzzles were challenging while Uncharted 2's puzzles were very simple.

Better intro: You were actually doing somthing in Uncharted 3's intro rather than just walking. Also had a quite shocking ending to the intro.

Better graphics: Better lighting and much better elemental effects added to the immersion in Uncharted 3.

Uncharted 2 Pros:

Better pacing: Uncharted 2 ramped up the action nicely and more quickly than Uncharted 3 which was a slog to play till an entire seven chapters into the game.

Better stealth sections: Uncharted 2 had some good stealth sections that were missing in Uncharted 3 where every stealth sub section devolved into an encounter.

Better boss battle: I say battle because both games have terrible boss fights, but the Chopper battle on Nepal rooftops in Uncharted 2 is the only good boss battle in these two games.

I think Uncharted 3 is better than 2 if you consider everything.

For me U2 had better enviroment design, characters and story. And that gives it an edge. And I'd put to question your point of "better set pieces" cause to be honest The burning Chateau is the chapter I hate the most in U3. I did not like that design.

I definitely think U2 is better than U3 but U3 was still a fantastic game.
People usually bash U3 for no reason.

I respectfully disagree. 3 shipped with awful shooting mechanics that they had to patch a few days in (as an early buyer this soured the experience for me).

The story was good...until the end. It felt like 90% of the way through they went 'oh shit we need to wrap up the story' and abruptly stopped it. I was sitting g there with my controller after the final villain just sort of rolled over and died, and said 'that can't be it..' and then, yup, that was it, roll credits.

Also I found the warped vision sections to be so frustrating.

Indeed! In fact UC3 >>> the rest of the UC saga!

I know this is a minority opinion, but I agree.

Both are amazing.

I was personally more entertained by 3's story, but I felt 2 was more polished in gameplay. Overall I'd give 2 the win because of that.

2 > 4 = 3 > 1

To me they're about equal but i have more love for UC2 because it was such a big leap from the first.

4>2>3>1

I respectfully disagree. I actually think 3 is the weakest of the series.

I just summed up my thoughts in another thread so I'll add them here:

Drake's Deception is a gorgeous game, but the shooting and moving mechanics are awkward, melee combat is clumsy, the final boss battle is a joke, the story seems recycled, and there are far too many sections where we as players are asked simply to press forward while some scripted segment unfolds - walking through the desert being the most egregious example. Drake's Fortune is excellent and Among Thieves is outstanding, but, to me, Drake's Deception was a misstep, narratively and mechanically. It feels like Naughty Dog focused on the negative parts of Uncharted - scripted platforming, cinematic pretensions - and moved away from the positive parts - improvisational gunplay, smooth and seamless moving and shooting mechanics.