I've beaten the game for the jedi ending, have not done the sith ending yet (yes there are 2 endings for those that do not know)!!!
Regarding what you said about the Jedi, other games (Jedi Knight series especially) and novels have revealed that several Jedi survived through the time period. Basically the movies just alluded to that Yoda and Obiwan were the only ones known to survive. But if all you know about is yourself, you kinda are the only one to survive.
Overall i really enjoyed teh game too, as you said it fills gaps in the story between ep III and 4 and does it nicely. There is definately the question about what happens to Kota since we never see anything of him in the later movies (sequall game perhaps...?).