I finished the Republic story of Shadow of Revan with my Jedi Knight. Shintar was right, the Republic version does make a little more sense than the Imperial version. Things are explained a little bit better in the Republic dialogue.
It's still not a very good story, but at least it's logical now.
I did find it interesting how, even though the missions and cutscenes are the same on both sides, the dialogue is different. For example, on Rishi, the pirate faction you belong to is different. Imperial characters belong to the Howling Tempest, while Republic characters belong to a different gang who everyone thinks are cannibals.
So even though the stories are the same, they must have recorded at least twice as much dialogue as scenes. You always hear that voice acting is the big cost in SWTOR, but maybe this means that it's really the missions and cutscenes which are expensive, rather than voice actors.
Overall, I don't think I approve of the way this Bioware team handled Revan. Revan was the signature character of Knights of the Old Republic. He deserved a better ending than being a random crazy Force-user boss. In some ways, I feel the current Bioware team was disrespectful of the KotoR Bioware team in their handling of Revan in this expansion.
I think this expansion was a missed opportunity in terms of story. I mean, why not spin a story around the Revanites recruiting the main character? After all, why wouldn't Revan want to ally with Jedi or Dark Council member, or character of similar status? Such an ally would only help his plans. And then, there's a lot of places you can go from there. I think a story like that would be a far more suitable Chapter Five story than what we got.