I was thinking about this not that long ago, and here are my thoughts:
A lot of space in games comes from FMVs, generally games done by Nintendo don't utilise a lot of FMVs. This is probably due to the N64 using cartridges and that might have set a precedent concerning how many FMVs are in 3d Nintendo games.
SSBBrawl came on a dual layer disc, MP Trilogy did and so will Other M. The Last Story almost certainly will (Lost Odyssey came on 4 discs, if I remember correctly). I'm pretty sure Zelda SS will as well, Zelda TP had a decent amount of FMVs considering it had to fit on a Gamecube mini disk, so I'm sure Skyward Sword will have more and possibly orchastrated music or voice acting, all which will take up more space. It could also possibly due to not many Nintendo games having extensive voice acting.
It's also worth noting that Nintendo have always made their games relatively small size wise, just think about how little games came on 2 GC discs, I can think of Tales of Symphonia, Resident Evil remake, 4 and zero, both Baten Kaitos, Zelda WW (one was a bonus disc though) MGS Twin Snakes and that LotR RPG. Even then, most were 3rd party and DVDs hold roughly 2x as much.
