It is interesting how sequel syndrome appears in the list. Portal 2 in my mind is not better than Portal 1, more refined yes...the mystery and innovation was gone. Same reason Bioshock would be on the list for me and not Bioshock 2 even though 2 was a far more refined experienced. On the other hand, Borderlands 1 was far inferior to Borderlands 2, though I might give it to General Knoxx.
I absolutely agree, although I think Bioshock showed greater craft. Bioshock II was far more explicit in its critique of Collectivism where Bioshock was implicit in its critique of Objectivism.