2>=4>1>3
I'm having a hard time, right now deciding whether 2 or 4 is better.
Uncharted 1 was a very simple adventure game. Everything takes place on the same island for better and for worse. I think the mystery part towards the end was one of the better in the series, a good introduction. Gameplay has issues.
Uncharted 2 was perfection. The gameplay felt perfect, everything Uncharted 1 was, but perfected. I felt that the melee was perfect for what it was. I feel the later games did a lot more with melee, but it didn't quite feel like it was there yet. The pacing was fantastic. I can't think of any game that had better pacing. Always felt like there was something. The train level, falling skyscraper, helicopters, these were amazing. They feel more genuine than Uncharted 3's set pieces. The gameplay felt perfect, the story felt great. The story wasn't some deep adventure, but it was absolutely brilliantly told. Loved the train for so many reasons. Love the fact that we start on it, climbing up. And we find ourselves catching up to the story, and find ourselves on the train again. Maybe it hasn't even quite clicked at that point, but when it does it's awesome. The set pieces in Uncharted 2, they feel deeper than they do in 3. I loved it and played it 10 times start to finish. And quite frankly I could keep going on about what I loved about 2, Tenzin levels, Jeff, and more.
Uncharted 3, felt like it was trying to make Drake's story a much deeper one. But I feel like it didn't quite get it. The first time I played, Cutter for example just felt like a random guy. Which seems like a poor introduction to a character who you spend the next several chapters with. Honestly, playing the second time makes the game feel better for this and a few other reasons. The most bothersome part in the game was during the shipwreck section. It just felt like a really long section just to set up a set piece. Like an hour, hour and a half of the game in this one part. I think the only thing that really ends up happening during this section was that we find out that Sully is not actually there. Aside from that, the ship set piece, though it's really cool; doesn't feel as genuine as the set pieces that we had in Uncharted 2. It feels avoidable. For me this section, was the only section in the entire Uncharted series where I was wanting it to be done. Aside from that, the game is very good; a little different at times, but it's great.
Uncharted 4, now that I'm thinking about it is difficult to place. I feel like it does a much better job at making a deep story than Uncharted 3, which set up the story for it. It also feels like for the most part it has some of the best pacing in the franchise. Uncharted 2 still easily tops it pacing wise. There were some parts that felt longer than they should have been, but not to the extent that I felt in Uncharted 3. Melee feels mixed here. In some ways it feels better than 3, and other ways it feels worse. Don't know how to explain it. One complaint I have with the melee is that there were some fights where it almost felt like Nate was being held back. Like for some reason, he isn't as good of a fighter when he's fight Nadine as he usually is. Which feels off. There was some great character stuff here, with Elena, Drake, that was amazing. Shooting feels great, just like it was in 2.
I think overall right now, Uncharted 2 is probably on average a better game personally, but there are a couple of incredibly fantastic moments in 4 that probably put it up to a tie.