I loved the ending. Honestly, I really wasn't upset about the lack of explanation. For one thing, we all know how good the Monolith team is at explaining techno-babble! Seriously, do you really want to see Shulk sitting in an armchair for 4 hours spouting gibberish?
As for Fiora:
It seemed pretty self-explanitory to me: Shulk was able to reconstruct an entire world, so one person's body seems fairly trivial by comparison. The who realization that Fiora got her body back was the final "twist" they were using as a mechanic for the ending. They wouldn't have been able to do that wonderful "looking through her eyes" ending that they did without it. I loved it.
As for the holes and questions? That's excellent sequel fodder! If they wanted to, they could now very easily tie the game into Xenosaga for the sequel. It deffinitely lends itself to continuing in a more space-opera direction now. Not that we really NEED another space opera, or even suggesting that Monolith is very good at space operas (I never found Xenosaga to be that well done, myself). But the material you find out at the end definitely is interesting, and could be explored more thoroughly. But I think it's good that it wasn't in this game for precisely the reasons you gave: it's so huge, it would have really taken away from the imminant story that was going to with the current characters.