When Quaritch organizes a pre-emptive strike against the Tree of Souls, the mountains were floating on their own while the RDA vehicles needed engines to fly, why?
The Hallelujah mountains float because they're essentially large chunks of unobtainium, which is a room temperature superconductor, thus subject to the Meissner Effect. This causes superconductors to "levitate" in the presence of certain strong magnetic fields:
Vehicles need engines to fly because gravity and the laws of thermodynamics still exist in the Avatar universe. So vehicles still need a power source for propulsion and can't defy gravity for no apparent reason.