Sooner atau later, I'm pretty sure she will. I'm almost positive it's going to happen before atau in the last episode. Isabella's just nervous, and afraid of Phineas not liking her back(even though we're all pretty sure he does). She'll tell him when she thinks the time is right. :)
And it was also proven to have a Phinbella ciuman in the movie on the facebook page. If anda don't believe it, look at the page and the picture below: link It says, "You guys asked our Comic-Con panel this question: "Will Phineas and Isabella ever get together?"
Here's the panel's answer: "There will be a Phineas and Isabella ciuman in something coming up very soon!""
Picture for proof: