I'm weird in that I even like 1 (and probably 4, but I need more time with it first) more than 3. I've got a few problems with 3.

While yes, it does have better melee, I don't consider that a good thing, because there was too much focus on melee, and I honestly just don't like melee in Uncharted. I like shooting and climbing. Same goes for puzzles. Better puzzles, yes, but I don't really want to spend much time on puzzles. I also didn't like how slow and handholdy the intro to 3 was. 5 chapters in and it's still giving tutorials. 1 and 2 started off quickly with lots of shootouts and ended up being more fun to start. 4 suffers a bit from that too.

I also don't think it flows very well either. You're jumping from location to location way too much. London, flashback to Colombia, London again, France, Syria, Yemen, then wherever the ship graveyard is, etc. From Chapter 5 onwards in Uncharted 2, you actually travel to where you're going yourself (except for when Drake wakes up in Tenzin's village, but that's close to where he passed out), and not just between chapters or through cutscenes, and I really like that. Same goes for Uncharted 1 from Chapter 4 onwards.

But the biggest thing is I'm not really fond of the desert setting. I like the jungles, cities and snowy parts of the other 3 games much more. Plus, 2 has the best final boss.

It's really hard for any of them to beat 2. It's the perfect Uncharted game to me, and is in my top 5 favourite games ever. 3 is definitely still really good, but it's my least favourite in the series (besides Golden Abyss, of course)

Nah, Uncharted 2 was easily the better game. Uncharted 3 was just a regurgitated Uncharted 2 but didn't feel as refined or exciting, it's still a good game in its own right but failed at invoking the same of sense of awe.

I think we're the same person 

The shooting and moving mechanics in Uncharted were never strong points tbh and I didn't feel 3's mechanics to be any better or worse than 2. The melee combat in Uncharted 2 is also very clumsy but unlike 3 its also visually unsatisfying, Lazaravic wasn't a terribly exciting boss fight either, the story in 2 was predictable throughout while 3 had some nice plot twists that were interesting. I agree with those scripted movement sequences and Uncharted 3 has many other glaring flaws but everything considered its better than 2 to me.

No, I disagree as well. I found Uncharted 3 to be the weakest game of the original trilogy.

Uncharted 3 has better puzzles than any other Uncharted game by a long shot.

That said, its fights are significantly more frustrating and trial-and-error-oriented than Uncharted 2. That one battle on the ship ball room where you basically just have to memorize where enemies randomly show up still annoys me to this day.

Also, while I realize Uncharted requires significant suspension of disbelief, that one part where Nathan Drake walks through a desert for three days with no water and then somehow manages to pick up a gun (still horribly dehydrated, mind you) and proceed to murder tons of people like it was nothing broke all suspension of disbelief for me.

I agree with this and would also like to note that Uncharted's quality follows a reverse Indiana Jones order.

I disagree with everything expect stuff like better melee or better puzzles.

And Nepal is easily the best set piece in the whole series in my opinion. Perhaps the most memorable in any game I've ever played.

And something went really wrong with the shooting mechanics in Uncharted 3. It's behind even the first Uncharted.

I agree with the op.
Uncharted 3 Singleplayer > Uncharted 2 Singleplayer
Uncharted 2 Multiplayer > Uncharted 3 Multiplayer

Uncharted 2 had more memorable moments for me. I also prefer Nepal over the deserts. The Chateau was awesome but it just doesn't beat the train sequence. The story and characters in the second installment where also better.

Gameplaywise Uncharted 3 takes the cake especially the combat. Guns feel way better in the third installment and graphics greatly improved. But plotholes and pacing issues make the experience not as good as UC2. For instance where do all those freaking spiders come from. But puzzles are way better in U3 especially the light/shadow puzzle.

For some reason, the aiming just felt off in Uncharted 3. Maybe it was just me but I had no problems in either of the first two (haven't played much of U4 yet).

Even overlooking that issue though, I still like Uncharted 2 better than 3.