Ok first off, if you remember TESB, Yoda says he has been training jedi for 700 years. Now if I remember correctly, doesn't KOTOR start 4,000 years before epi I? Sort of makes that unlikely. But the tree idea is something that definetly should be explored.
As for story development, I think the idea of starting on Courascant is a smart idea. It allows you to start where it all started, where the Jedi Council first delayed action during the Mandalorian Wars, which led Revan and the Exile down their respective paths. I think possibly also having the final cutscene occuring there would also be smart.
As for characters, I don't know if having so many returning characters would be such a good idea, seeing as through the first two games there was the option to kill most of them. Have some come back, but only the ones who you didn't have the possibilty of killing. Maybe Bastila, but more likely Mira, and you can follow Kreia's vision that she dies protecting the planet.