We preferred the Fountains layout to the Lakes layout....but to be fair, we were comparing a two bedroom in Fountains to a premium one bedroom in Lakes. Things like the layout of the kitchen and master bath, and the overall decor, were just more our styles in the Fountains villas, but were completely acceptable in both sections.
Lakes has elevators, if stairs are a deal breaker for you. We prefer (and always request) top floor villas (love those skylights, and both sections have 'em) and the elevator access in Lakes was a nice treat for tired legs.
We like the fact, though, that the Fountains villas have stairs from both the front entrance and balcony. In Lakes, obviously, you can only enter and exit the villa from the front.
Lakes does, if I am correct, have slightly higher yearly maintenance fees than Fountains.
Some of the Lakes buildings are closer to the Fountains pool than some of the Fountains buildings, so location is good (but you will want to avoid any Lakes buildings that are close to the I4....noise could be problematic).
If the Lakes villa you are looking at is a lock-off, it would probably give you better options for trading than a standard Fountains 2 bedroom. Not sure what configuration you are considering, but thought I would mention it just in case.
Hope that helps! Let me know if you have any other specific questions!