The plot can usually be summarized as:
...
It seems to me that a lot of science fiction has an anti-science bent.
You could just as well say that all non SciFi has the same problem... Govenrment wants to do something stupid and only the maverick politician can save the day; Spouse does something stupid and only two hours of dramatic avoiding-the-real-problem can reunite the couple; Boy wants girl but it takes 90 minutes of wacky adventures and two near-death experiences before he gets the courage to ask her out.
The "best" SciFi doesn't make science out as the villain or the hero - Instead, it shows us the (possible) realities of everyday situations in a setting that extracts those problems from the limitations of "modern" science... ie, The boy will still take 90 minutes and nearly die before he gets up the courage to ask the girl out, whether he lives today, or in a dirt hovel 300 years ago, or on a colony station orbiting Jupiter in the year 3517.
I think your real complaint applies to most forced-plot movies in general... You need some artificially-induced source of tension, followed by stalling and CGI to make the story last more than five minutes, followed by a completely predictable but somehow "unexpected" resolution to the original problem. Faux-science just happens to make for some good villians without needing to really justify their motivations. Why does the god-like AI want to enslave humanity? Because, um, er, humans look weak and inefficient (and what about dogs, trees, ants, and every other lower life form on the planet that A, humans don't see a need to enslave/exterminate, and B, we must look barely better than them to this god-like AI?).
So blame Hollywood, not SciFi in general. :)