I would say the "best transportation" would depend on the parks you intend to visit most often.
Everyone has to take a bus to AK. THe ride from AKL is pretty short, though.
Epcot resorts offer a walk to Epcot, boat/walk to MGM, and buses to MK.
MK resorts offer a monorail to MK, monorail to the TTC to catch another monorail to Epcot, and buses to MGM. Contemporary does offer the option of walking to MK and the Poly allows you to walk to the TTC for the Epcot monorail.
WL has a boat to MK and buses everywhere else.
The moderates and values use all buses to the theme parks, but some have their own buses, which may make them less crowded. Both Port Orleans resorts offer a boat to DTD. So does Saratoga Springs. The other resorts on property would offer a bus to DTD.