The only things RG has on SoA is some decent weapon / item / skill crafting systems and action-y combat (which might not even be as solid as SoA's, which is turn-based but often excellent). SoA has WAY better environments (especially its awesome world map), characters, story, and audio. Both games have some pretty good side quests and a cartoon aesthetic hat holds up.
Yeah, I really enjoy both games (I play layer Rogue Galaxy last year and liked it just fine; I played SoA for the first time in high school, at least 10 years ago), but Skies of Arcadia is better.