A little late, I realize, but I had to finish college before playing this amazing game. So, read as you will.
I think that Portal 2's greatest adversary is Portal, or at least the perception of the first game. Let me talk about that perception and what I think (hereafter considered "The Truth"). Portal and Portal 2 are great because they set expectations, reverse them, and are still true to themselves.
Okay, heady analysis incoming.
However, the puzzles are only minorly dynamic with the story. Think about it. If we consider the escape sequence to be Chell acting of her own accord with her own goal (destroy GLaDOS and/or escape), then only the most rudimentary of the skills in the test chambers themselves are useful in this sequence. Most prominent in the escape is the new "rocket" tool. Otherwise, you are simply placing portals where the walls allow you to (see escape sequences in Portal 2), timing mechanical crushers, and occasionally using the "momentum fling" move.
The tests, then, are complicated in a way the escape never is, and that is exactly the point. GLaDOS, as shown more clearly in Portal 2, is frustrated by your continued success at her tests, so she tries to throw you off. But, in all honesty, playing Portal again recently, the final puzzles are not all that difficult, no matter the crazy solutions people have devised. I think this is somewhere people look back on Portal with rose-tinted glasses. It was not and is not a difficult game. Its most challenging puzzles were outside the narrative as DLC. The game itself is remarkable for its teaching rather than its difficulty. Portal can be conquered by basically anyone because the game so acutely teaches the player how to think with portals. You conquer GLaDOS because Valve helps you to do so. Your only adversary is your own intuition about what to do next, an obstacle which Valve helps you overcome. Great players can do what Valve does not expect. But non-geniuses like me can play the game as Valve expected, and the enjoy the hell out of it.