I always preferred the Dark side ending.
In the Light side ending all Kyle does is carve a statue of Qu Rahn and Morgan Katarn (yeah, great LEC...).
THey could've made something of Kyle and Jan (I dunno, maybe a love interest - that would've been good - it's a shame they ditched Jan for Mara in MotS).
The Dark side ending does, as Tycho correctly put it, depict Kyle as the new Emperor, and was altogether better.
I think they should have made MotS have two seperate beginnings, dependant on which ending in JK you got - that would have made it a lot better. (and they should've given it high-res sound! Ugh, its all muffled!)
- My Personal Starcruiser.