Interesting mod, lots of potential! Nice voice splicing, by the way. Most of the lines are super recognizable for those that played this game bazillion times, but they're still fun to hear.
Although this mod certainly adds to the replay value, at this stage I feel the Genoharadan faction is way too similar to the Exchange. They have the same base of operation and the storylines are directly linked. The new fight sequences and additional dialogues are nice but don't feel particularly refreshing.
Completely separating the Genoharadan storyline from the Exchange storyline and change its base of operation to another planet (something like Telos surface military base) could potentially boost replay value. I would suggest adding some motivation for the Exile to go after Genoharadan. Perhaps instead of the Exile being kidnapped, its one of his/her companion like Atton that's kidnapped. And despite Kreia's disapproval, the Exile decides to go after the kidnapper and is lured to another planet for a final confrontation.