Uncharted 2 benefited from the "refined sequel" syndrome. The first game did most the heavy lifting, leaving the sequel with a lot of room to perfect its formula and push its limits both creatively and technically.
Arkham City is currently benefiting from the same thing. Bioshock Infinite will likely be the next example.
Uncharted 3, on the other hand, has little room to grow technically..it has to rely on its script in order to deliver an experience that is simply more enjoyable, even if it's technically very similar. Lower scores are almost entirely the norm in this stage of a franchises life, even if most still herald the entry as the franchise's best. Most recent example would be Gears 3..maybe Rock Band 3 (haven't checked this one myself). It probably has something to do with the initial impact. The post-game breathlessness, if you so please.
That Uncharted 3 is probably STILL going to hit 95 on the metacritic is a massive surprise for me. I expected lower scores..but I still expected most people to say this was the best one.
Things are funny that way. Popular trilogies tend to be that way throughout any medium (so long as the third installment actually turns out good), or any successor to a wildly successful movie/game/book/tv show..etc. It'll probably happen with The Dark Knight Rises, for example.