I just want to start off by saying that I think this is a great game, but I think it might be a tad bit overrated.  Metacritic has it at a 88, but I think low 80s/high 70s is more like it.

Anyway I have some gripes with this game.  I am sorry if some of these have been discussed to death, but I have avoided most of the press on this game until now.  I will try to list them from the biggest problem to the most minor:

1) Enemies take way too much damage.  This might be okay from a gameplay perspective, but the game really excels at story and atmosphere, and you get totally pulled out of it all when you have to cap a pirate in the chest a solid 10 times before he goes down.  I find I just end up going for all head shots.  Ugh.

As an aside: I find it funny that people often claim that videogames "train" people to be gun-toting killers.  Well, considering most games reward you for aiming at the head, they are going to be training a bunch of storm-trooper-esque crap shots.  In reality, you aim for the vitals in the chest.  Anyway, I digress.

2) Plexiglass everywhere. I hate when games prevent you from going places by sticking up an invisible wall.  I know it makes level design more visually appealing while keeping the gameplay funneled and directed, but it is really annoying when you are trying to search nooks and crannies for the treasures that are scattered about.  Okay, so I can go behind this tree but not that tree.  One ledge I can climb up, but when I try to climb another similar ledge, Drake jumps up weakly and raises his hand like a moron.  You know, I have a lot of problems with GTA4, but one thing that game definitely gets right is that if you see something that looks climbable, you can climb it.  If you see a location, you can go there (excepting the ocean, of course).

3) Unpredictable quick-time events.  I effing hate these, always.  They are never good.  They are never, ever, ever, ever, ever good and they need to die in a fire.  The reason they suck so bad is A) they force you to be on edge for every single cut-scene and prevent you from enjoying the cinema or B) you are not paying attention, die in some retarded fashion, and have to redo the QTE.  So gamey.  So lame.

4) The jet-ski mechanic is not very good.

5) levels too often fall into the following formula: Climbing puzzle -> battle in arena with cover -> do some corridor navigating and perhaps solve another puzzle ->go back to previous arena and battle enemies coming from a different direction -> repeat.  Some of the best parts of the game, in my opinion, are when this formula is broken up.  For instance, I have encountered two climbing sequence where you have to pick off some enemies while hanging.  Those were fun and a little different.  The extended puzzling sequences are also a lot of fun.  Granted, I am only about 60-70% through the game so things might change, but I am getting tired of fighting in the same set-piece arena 4 times before moving on.

Anyway, feel free to flame away or add your two cents :)  I actually really like the game, but those issues really stand out to me.

After playing Uncharted 2, all of these problems seem so much worse. I actually went back to finish the game on Crushing because I'd loved Uncharted 2 so much and had done it on there... but fuck me. This game, which was ok before hand... now just seems fucking broken. I know they wont, but I really wish they could patch it to play a lot more like Uncharted 2, most of the times I die because bullets clip walls, or Drake wont pin to cover or he wont turn on cover... it's just so fail, especially after the near perfection of the second game.
 
It's a shame to, as I'd love to finish it again.