Hi Michele,
Decisions, decisions! I have stayed in a 2-BR unit at both of these resorts, and given these choices I would choose Animal Kingdom Villas without question. Having just recently stayed at the newly opened Kidani Village at Disney's Animal Kingdom Villas, I can tell you that these rooms are spectacular, large and boast an additional full bathroom (making three full bathrooms for a 2-BR villa). The pool area is by far a more toddler-friendly, with lots of squirting fountains and splash areas.
To be fair, the things that didn't thrill me about this resort is the remote location, and the lack of quick service dining. It is 5-10 minute walk over to the Animal Kingdom Lodge to get a quick service meal. We also found ourselves walking over the the main lodge to use the playground and Savannah viewing areas. We had a rental car, and this made the remote location tolerable for us.
Old Key West certainly has a fantastic centralized location, with boat access to Downtown Disney which are the greatest benefits, in my opinion, of staying at this resort.
I suggest that you visit
www.allearsnet.com to view their extensive photo library of every Walt Disney World Resort. I have always found it extremely helpful when trying to make a resort decision. Simply click on "accommodations" to find them.
Hope this helps, good luck with your decision!