I finished ToS a month ago, and let me tell ya, when I was done I REALLY wanted to just play it again. (Especially with some of the goodies they offer at the end of the game...and that's with about 80 hrs. logged into the game.)
I started Skies about a week ago, and it's going good. It's fun; although there are way too many battles and time between save points, and the camera is pretty crappy. However, I think I would have enjoyed it more if I played it BEFORE ToS, because of a couple of reasons. 1. Aestethetics. ToS, just looks so much better, as is expected to be, because SoA is a port. 2. The sound really lost quality in the GC version compared to the DC version, and sounds unbearable sometimes, when compared to the ToS sound. 3. The game-play is slower (because it's Turn-Based), so when you're coming off a fast-action battle system like ToS, it's harder to adjust to your normal turn-base battles. 4. The camera is pretty shoddy in SoA. It can get annoying.
However, these are really very minimal annoyances in a great game;the type you really only might pick up after playing a crisper packaged game like ToS.
Both are great if you're an RPG fan. I had so much fun with ToS, and I'm about 20 hrs. in in SoA, and so far it's really fun as well.
I say you play Skies first, for the reasons that they're both great, but you'll get more enjoyment out of SoA.