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.