Yeah, if it's any help, I own the DC version and now wish I would've bought the GameCube version, due to how much time is wasted in the battles on the DC. SoA Legends is something like HOURS faster than the Dreamcast original. There are a few minor setbacks in the GC version, but more content was also added.
If you're buying solely for playing, I think Skies of Arcadia probably has the upper hand here.
For collecting, looks like RAD is the better choice?
Purely speculation, but I think Skies of Arcadia has a somewhat likely chance of being re-released in a future collection, but we might not know for a while. Or until March 30th, at least.