The plot is messed up, it is that way for a reason. Tim Kring has his writing gear in line, and will give you what you need. At the end of the last season, almost everything was tied up neatly into a little box, and you had that "ahh, at last, I know what's going on, and that everything is going to be alright" feeling. Now as you delve deeper into the rabbit hole, you find out more about the company, and whether they are actually manipulating Dr Suresh, or whether the veteran Noah has got his facts and figures right. Bob really perplexes me, I have no idea whether he is truely manipulative, or truely has everyones best interests at heart. Hiro and Adam may be a forgone conclusion, but the interest does not lie with that battle, it lies with the battle before hand of nathan and hiro, and whether nathan talks sence into hiro, or visa versa.
Again, what the hell is going to happen is anyones guess, let's watch and find out, rather than slag off a brilliant writter who is trying to save a foundering channel!