LBV has a more resort course feel to it since a number of holes run through Old Key West and Saratoga Springs. Magnolia has more natural surroundings. Magnolia is a little more challenging. The course conditions have always been excellent on both. Of those two I would lean towards Magnolia. I know you didn't mention it, but I like Palm the best of the current WDW courses.
It's a shame WDW let the Bonnet Creek courses go, Eagle Pines was my absolute favorite, and the renamed Osprey Ridge (Tranquilo) for the Four Seasons is a nice course, but not for the prices they charge for it now.