Well, one way I can think of to start with both Revan and the Exile, at starting levels, and able to set the light/dark side path from earlier games is the following...
Start of Game - Select portrait, stats, etc for your character. Both would start of at least as Jedi, or even one of the prestige classes from KOTOR2. Either give a set of bonus feats and skills based on the class choices, or additional points/special feats to represent their past experience (like 'War Veteran' in 2). This basically covers deciding who/what you played in the first games.
Why are they weakened? Basically they found the Evil Sith Empire. Either the Sith somehow stripped them of their powers or otherwise cut them off from their access to the force, or the area of space their empire is in somehow disrupts the flow of the force.
The game starts with them captured by the Sith and interrogated. The course of the interrogation would basically outline your choices from the first two games as far as lightside/darkside, who you killed or saved, and who you trained as Jedi, etc. The Sith ask about your past, your allies/enemies, etc. Or if you 'refuse to speak', you still make the choices as the questions force you to think about the past. Which might be better, actually, since you could insert short cut scenes showing light/dark side versions of the characters, and if they died show them falling, etc.
After this, the characters are thrown into cells, manage to communicate with each other and work together to escape. (even if they're opposite alignment, I think they'd work together at least that much).
Gameplay after this has a few options.
1) The two stay together, but the designers find a way to force them into splitting up when they get to main missions (I'll take my group to fight through the forest of Endor's moon to turn off the generator, you take your group to infiltrate the death star). They could either do this on the same 'planet', or have them split up because two problems emerge at once, and they need to deal with both. They'd either need two ships, or to drop off someone and come back (which could lead to a rescue mission at some point).
2) The two go their seperate ways, either working to the same agenda (both the same alignment), or working to cancel each other out (opposite alignment). What one character does in a place the first time can have repercussions for the other character if they go to the same place later, or just have two seperate storylines with seperate sets of planets (or some seperate planets and a few shared).
In the end, your two PCs band together, to fight the big bad Sith guy. Of course, if their alignments clash, you get one big problem that eventually they're going to have to have a confrontation at the end, since only one 'side' can win out. In that case, I'd think you'd basically have to pick which character you want as your main one in the final duel, and play as them, abandoning one of your characters. Which actually might give you something like the emotional impact of the big 'Revan Reveal' from KOTOR1.