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)
