[For Light Theme] What if, say Revan is the Master and the Exile is the apprentice but the Exile has abilities/saber skills/powers much like Obi-Wan as a Knight and is capable to take on an apprentice of his/her own. You would create a character much like KOTOR I & II. As the game progresses and you align with the light side, you successfully locate and greet the both of them and discuss about the Sith Empire. Revan is killed by a Sith and the Exile takes you on as an apprentice. I would rather have Revan be alive as the Master because the whole "wound in the Force" thing with the Exile is somewhat complicated. Or maybe the Exile is captured by the Sith and is turned to the Dark Side and must be stopped. Bastila returns after being with her dying mother in Coruscant. During that time she has taught Mission Vao and Zaalbar about the Force and are now Jedi Padawans. Admiral Carth would also have a touch in the Force but isn't focused enough to use it, yet. Juhani and Jolee search for Revan only to encounter your character along with the group from KOTOR II. If Revan is alive as the Master, they all return to Coruscant and reunite to discuss events leading up to the search for the true Sith. If the Exile is the Master, they still return to Coruscant and discuss the matter about the true Sith only to discover that the Exile killed Revan and is masking his true intentions and his character much like Palpatine did just to get an inside job and really stick it to the Jedi once and for all. The reunited "Lost Jedi" will not survive. Some will die early from battle, some from sacrifice, or maybe one to three will turn to the dark side.
Another wild idea: Revan and the Exile have turned to the Dark Side from the beginning, Both KOTOR I & II groups are one as you lead them to search for the Sith. Several members from your party will fall to the dark side and join them. In your search in the Outer Rim planets, you encounter a very young Yoda. He's brought to Coruscant and immediately rises in the Jedi ranks. Yoda becomes a Knight at a critical point in the game and is dispatched to aid you and what remains of your Party.
[For Dark Theme]-- Revan=Dark Lord
Exile= Sith apprentice to Revan
main character= becomes apprentice to the Exile after Revan is
defeated by the Exile.
Bastila= leads the effort to defeat you due to her past "association"
Carth=leads the effort to defeat you due to his past "association"
KOTOR I group= enemies due to past association with Revan.
Kotor II group MINUS Mandalore, HK,T3= allies due to association
with the Exile.
Mandalore= Flees and reunites Mandalorian clans in Dxun. Secretly
aiding both Jedi and Sith in the hope to weaken both
simultaneously and finish off the last of the two
Order still standing. HK aids the Mandalorians due to his
past association with his dead Master, Revan
This would be a mainly dark theme where the objective is to seek, plunder, discover the True Sith, lure force sensitives to the dark side and annhilate every Jedi, the Rebublic, and punish the mandalorians for their audacity. Main goal is simply to conquer the galaxy and bring the rise of the Sith Order.