This finale was very appropriate for this season. I don't think very many people understand that this was not meant to be a SERIES finale. This show was canceled.
With that said this season made it clear that Jude was very dependent on Tommy. Even when he was not in her life, he still affected her. (SPOILER)---> I.E. he was in her head when she overproduced her CD.
She had to overcome this and look into herself to really be able to make music that was great and that wasn't cluttered. Hence why the basement song was so important, it made her realize that. In the end had Jude not made the decision she did, she would not be able to grow. Which is the basis of this show.
Now Tommy will always be an important part of her life, hence why only he could help her finish the CD. If this show went on longer or had a movie, it would end the way everyone wished it would. But this ending for this season finale (that later became series finale) was natural.