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.
I have been messing around with the excellent Lost Modules resource, and would like to do something with the 2 most complete maps. The Czerka base on Korriban is pretty complete, and can be seen in some early screenshots. The cut shadowlands level is also usable, though there isn't any indication of what it was for. It is probable that content from the shadowlands was moved out of this module to reduce its size (this is obviously entirely speculative).
I thought about NPCs that were underused, and immediately went to Garrum and Tar'eelok, the cut NPCs that duel with Vibroblades in the Jedi temple. They have basically no role except to offer Jedi Code exposition. They also use alien voice overs which is the most important consideration.
The Czerka base is set up like a hallway, with a shield emitter at the far end, and the obvious plot involving a master and apprentice is to have the master get captured and the apprentice freak out. The Kashyyyk Shadowlands is also an excellent place to have Czerka dealing with the Sith outside of Korriban, as the Sith aren't really present on Kashyyyk, and it provides some interesting combat situations and potential conversation paths to turn less dedicated Czerka employees.
Considering all that, I came up with this general story outline: 1. The Shadowlands lift Wookiees mentions that some heavily armed Czerka employees recently went into the Shadowlands after a ship crashed. 2. Entering into the cut Shadowlands level (either inserted in between the existing levels, or as a separate area entered from another entrance), you are attacked by Czerka guards. After fighting through them (or convincing some to run away), you meet Garrum. 3. Garrum has killed a lot of Czerka Employees and a Dark Jedi. You find out that Tar'eelok was captured. You deduce that the Czerka would take them to Korriban, as that is were Czerka and the Sith do business. 4. You then have 4 paths to follow with Garrum: 4. a. Persuade him to go to Dantooine (Light Side) 4. b. Let him go to Korriban Looking for Tar'eelok (Neutral) 4. c. Persuade him to seek Revenge on Korriban (Dark Side) 4. d. Kill him for being (or because you're) evil and giving in to anger (Dark Side) 5. You then go to Korriban and enter the Czerka facility (with identification you found in the Shadowlands). 6. You fight through Czerka Employees and Combat Droids. If Garrum is on Korriban, you have to rescue him from a holding cell while making your way through the base. You then have another conversation. Garrum always stays back to recuperate and catch up to you later. You can push him towards the Light or Dark side in this conversation. 7. Upon shutting down the shield guarding the main room, you find a Dark Jedi and a Czerka Boss, with Tar'eelok in a force cage. Garrum catches up to you at this point. If you pushed Garrum to the Dark Side he electrocutes the Czerka Boss. Either way you fight the Dark Jedi (and the Czerka Boss if alive). 8. Tar'eelok's cage opens once they are both dead. If Garrum is Dark Side, Tar'eelok will be displeased, and piss off Garrum. There are multiple results for this scene depending on what happens: 8. a. If Garrum isn't there, you can let Tar'eelok go to Dantooine or kill her. She will be sad if Garrum is already dead, and may attack you if you say the wrong things. 8. b. If Garrum is Light Side or Dark Side and talked down, she will be happy he is controlling his anger, and they will both go Dantooine 8. c. If Garrum is Dark Side and not talked down, he can be allowed (or encouraged) to kill Tar'eelok. He then runs off 9. The player may return to Dantooine at this point. If either Garrum or Tar'eelok is alive they will appear. A few different ending permutations can happen: 9. a. Garrum and Tar'eelok are alive. They appear in the courtyard outside. Tar'eelok thanks you for helping Garrum control his anger, and he is now a Padawan (regardless of when you did it) 9. b. Tar'eelok appears in the courtyard outside. She is sad and doesn't think she'll take another Apprentice. She thanks you for saving her, but wishes you could have saved Garrum. 9. c. Light Side Garrum can be found in the courtyard outside. He will inquire about Tar'eelok. The player must lie, but he can say she died in the fighting, or was executed before the player arrived. He will be upset he didn't go to Korriban. 9. d. Dark Side Garrum can be found in a bar on Tatooine working to destroy Czerka for turning his master against him. He will run off to disrupt Czerka mining operations.
I think this is a fair amount of reactivity, but isn't actually that complicated in terms of setting up dialogues and events. It also gives the player a lot of potential results without feeling too contrived obviously. This is totally conceptual, but I think it makes a good use of these areas, and adds another mulitple planet spanning side quest, which are my favourite parts of the game.