Why are you so concerned about getting into a prominent undergrad school? Contrary to the popular opinion, it doesn't matter all that much. You'll graudate with a Bachelors' degree like we all will, and possibly apply for graduate school (I assume you are, since you're interested about MIT and such).
You'll be able to get into almost any undergrad school with those grades, which will give you that Bachelors' degree; therefore, giving you an almost definite admission into tons of graduate programs. Not all undergrad programs have the same classes or focus, but that's moot for the most part. The undergrad program I'm in is short of a PDE class, complex variables (actually, offered as a special topics course this semester), and a few more. I don't feel too worried about this, though. I'll have a chance to take these courses in grad school.
I had around a 3.25 GPA when I entered as a freshman. Has is it effected me in anyway? No. Do I plan on going to graduate school? Yes. Will my high school GPA effect my admission into the program at all? No.
Edit: This seems to be closely related with the issue of students and AP classes. I've seen too many times a student whose transcript is riddled with AP-this-and-that, 4.0 GPA, 36 ACT score, etc etc, who 1) has no "real" comprehension of the subject material 2) has no real "passion" about the subject, either. It's quite sad.