Basically everything.
Besides enemy design and AI (what you said/assumed about the combat is true; you must read the movements of the enemies and h.slash, v.slash, d.slash, thrust or shield-bash accordingly), there's a plethora of puzzles that use motion based gestures, items that are motion based in different ways like the remote controlled beetle, aiming of ranged weapons, the use of the sword for searching for secrets by motion control (dowsing) or 'drawing patterns on magic walls' and mini-games, and various other movements like flying, balancing on ropes and swimming.
Some movements could be fairly easily swapped for stick control like the swimming (flying would already be harder since there's various moves), but for everything else I guess they basically would need to rebuild the entire engine.
Which would result in an entirely different game; Skyward Sword is Skyward Sword because the motion controls are so integrated into every aspect of the game.
