Okay here's my full response and thoughts.
I completely disagree with removing the Hanharr/Mira sequence; I thought it worked great in TSLRCM, the only bad part is Hanharr's sudden disappearance if he goes off to fight Kreia, in fact that's the main problem with Malachor V IMO, no hangar for Kreia to arrive in- in the Trayus Academy and Party Members disappearing (Which is where that sequence when you seen them attacking the Academy and you're just behind them is great) I also think the remote's log of Bao-Dur's instructions should be kept but I like the whole droid V droid V droid, we got with TSLRCM perhaps the change I would make would be this:
-Bao-Dur dies, either at the Droid Factory or perhaps an apt place would be sacrificing himself on the Ravager to destroy it.
-Things happen, you step out of the Ebon Hawk onto Malachor's surface with the remote, the remote displays the instructions, you go around activating the M.S.G- at the final one just before the Remote activates the sequence the PC (In a cutscene) maybe hears explosions and runs to that cliff edge where they observe the party fighting the assassins. Fade to black, fade in on the remote by the terminal and then GOTO arrives and that part plays out like it does in TSLRCM depending upon what happened in the Droid Factory.
I have no idea where exactly the best place for the Mira/Hanharr encounter to happen would be, perhaps even before the Exile awakens-
then just after Mira/Hanharr leave; you could have the rest of the party (Excluding the Droids) run up to the big door that Mira and Hanharr pass through if they go to face Kreia;
-If Mira is with Hanharr they should just pass through the army (Let's say 20 NPC's for arguments sake.) like water, lets even say that Hanharr makes a fake prisoner of Mira and leads her through the crowd.
-If Mira survives and Hanharr doesn't Mira could simply just join the rest of the party when they arrive.
-If Hanharr kills Mira, he should be at the head of the "Army" (Because Kreia Life Debt) when the rest of the Party arrives and then perhaps the Exile, when they run to the cliff ledge could see a part member- slay Hanharr Atton let's say; whom then takes a penalty against when faces Sion because Mira died.
As for Malachor being boring, I'd liven it up with some Tusken Raider style tents maybe with Sith Assassins and such meditating by them on parts of the surface.
Or even, thematically you could have the surface improved by having it littered with corpses of both Mandalorians and Jedi- maybe even the entrance to the Trayus Academy could look something like this:
I don't know how this would apply to a dark side Exile that took on Hanharr and Mira died in the Jekk Jekk Tarr because I've never done that myself.