Isabella will probably tell Phineas her feelings about him eventually. I think she's just nervous about him turning her down and he's always so busy. If not for those two factors, she might have told him already. I'm sure that she'll definitely tell him eventually though it might take some time.
Sooner or later, I'm pretty sure she will. I'm almost positive it's going to happen before or 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 halik in the movie on the Facebook page. If you 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 halik in something coming up very soon!""