Unfortunately, many programs have a 3.0 undergrad cGPA minimum. This is often not set by the department, but by the graduate school - sometimes there is nothing the department can do about this. It really sucks, especially for somebody like you who has improved in a Masters program. I'm not saying you can't get in anywhere, but you may have to cast a wider net because of this. I'd suggest looking at the "sub-3.0 GPA success stories" thread in The Lobby section of Grad Cafe forums. There is lots of good advice from people in your situation who have been successful in their PhD applications. Also, what is your undergrad math GPA?
Also, since you asked for honesty: I think your undergrad GPA makes applying to Stanford, Harvard, or MIT a waste of money.