I feel the exact same way! I love Isabella/Bella to death! And even though I'm only 13, I can promise you I have liked this name way before it became too popular! I feel the exact same way about Nora, my all time favorite name after my grandmother, that is now becoming popular as well!
Its a toughie, because for me, I have time for it to grow out of style, then again, it may become overused by then. Right now its hopping, so your daughter will most definitely have another Bella in the room with her when she starts school.
My advice for your daughter is to go ahead and name her Isabella. I am the same way about unique names, but I have grown to realize that names are only reflections of who you want your child to be, and that naming your baby a 'popular' name doesn't mean you will love her any less, in fact, I think it will be much more special for her to know that for nearly 20 years you knew that your firstborn daughter would be an Isabella.
If you would like, however, give her a unique middle name, or give her two middle names. It wil freshen the vibe. I really like Bella Adare or Isabella Trinity. But I also like Isabella Marine, or if you want to give her two middle names to make it different, I would say Isabella Yvonne Telaina or Isabella Eden Leshae (Lee-shay).
If you really do not want to give your baby girl a common name, then I would say definitely incorporate Isabella somewhere in the name, because it must be so personal to you.
Congratulations on your first child, and keep us updated on what you decide about your situation!