These are just some ideas that I wanted to write down after going through the end game sequences again. I was using the Extended Enclave mod as well as TSLRCM, and overall I think it is better than normal TSLRCM, there is still some things that I think could work better.
First thing, I would have the Nihilus/Tobin cutscene trigger during your next space flight after completing Onderon, instead of when entering the enclave. It disrupts the flow of the sequence a bit where it is now. Handmaiden confronting Kriea and finding out she is Sith before the trial is awesome, and makes the whole scene way better. The scene where Visas confronts Kriea seems redundant though. I imagine it would be good if the player was female, but with Handmaiden already there it is sort of odd.
Everything else with the masters is awesome, and I really like having the Genharadan explosion stuff here. It fits pretty well, but it could use some more editing. The Sion/Nihilus fight is perfect, and I love having it here. The conversation with the party on the Ebon Hawk could use some retooling though. Handmaiden's "come with me" line added by Extended Enclave is totally out of place. It can just be removed, she doesn't need to say anything and they can cut straight to the ship. I'm fine with having Handmaiden not immediately trying to take Kreia to Atris. She seems pretty OK with her being a Sith in the first conversation, and doesn't stop her from killing the Jedi masters. The only thing that bothered me was Visas being here after confronting Kreia. If the earlier scene with Visas confronting Kreia was removed this would be fine.
I think the order of events could use some adjustments. There really should be a scene of Kreia knocking out the Handmaiden if she's the one that took her to Atris, so there is a reason why the fight with the sisters occurs after Kreia gets to Atris. Once Atris is dealt with all the attack space battle cutscenes should play out and we can have our conversation with Grenn, where he brings up Bao-Dur and HK-47 being missing. After this line is when the HK factory stuff should start. It doesn't work nearly as well right now, occurring after the factory is already over. You could then have the shuttle flying cutscene, come up with some excuse for Bao-Dur to die (shuttle crash maybe :), and have HK do the factory as normal.
I'm not sure how you could fix the weirdness that goes on with the Ravager. The shuttle boarding on the station is written so that Mandalore, Visas, and the Player are all together, and makes perfect sense. But the second they get on the Ravager, the player clearly shouldn't be there until after all of the proton cores are placed. I'm not sure if there is a satisfactory solution to this. Restoring the Citadel Station destruction ending would be cool, and I don't think it would be that much of a stretch to just show the shuttle leaving the Ravager, and then cut to the Ebon Hawk leaving from the polar cap instead of the station.