Applying to Ph.D. with 5 years in Bachelors
This sort of thing should be explained in the cover letter. This trend is pretty common; freshmen enter college ready to party, realize halfway through that their grades are actually important, and then buckle down and do good work for the rest. You simply need to state that, despite your initial behavior, you are fully committed to your education. Given a 3.5 GPA at the end, I don't imagine you would have too much trouble.

Do note that this will vary as a function of the universities to which you apply; some may take a harsher view than others. Still, you have a good explanation for the one bad year, so it shouldn't post too much of a problem for you.