You know how you could fix the very obvious flaw that Wind Waker had near the end, with that filler-ass filler of the triforce pieces?
well, with Skyward Sword what you have is essentially a 15-20 hour version of that very same problem in the back half of the game. Someone at Nintendo got some great ideas for how to reuse their 3 major environments and that person must've had something on Aonuma because that shit became way too long by the end of it all, including shit like making you fight the same major setpiece boss at least three times in that game with not much changing between each fight.
It's not going to take something like streamlining the water temple or making the triforce quest tighter that's going to fix SS. It's a major revamping of that stuff that happens when the game goes full Okami on your ass that they would need to fix, and i'm not sure they would be willing to make the cuts/changes necessary.