Personally, i think the "new" GladOS is just the logical conseguence of the first game.
All through Portal 1 you had this feeling something was off. True, GladOS wasn't really that good at scare tactics but the intention was there nonetheless. Then you get to the point where she actually tries to kill you, and shit gets real.
After that point it only makes sense for GladOS to drop the pretense. You know as well as she does that she is dangerous and she's out to get you, putting up a façade is redundant at that point. The whole part about her control over the facility doesn't make sense, i agree, especially considering it was never hinted at in the previous title, but then again if you're going to have an antagonist you need it to have means to endanger you, besides giving them a motive to actually do it.
SPOILERS AHEAD
That's why I also liked Wheatley's turn as villain. Because he feels more like the original GladOS at the beginning, only inept, and then he starts going mental, scaring you not by consciously trying to kill you but by being a massive incompetent with a lot of pent up rage.
IMO, portal 2 works very well. The puzzles are there they're varied and a substantial amount, plus there's DLC on the horizon that will also be free for the PC users, and even thoguht the plot can occasioanlly force the puzzles to take a back seat, it only really happens once and it just marks the transition from one set of puzzle mechanics to the next.
The plot is still just a framework for the puzzles, though it is bigger and more elaborate than before.