I personally hate controlling party members, mainly because I find them way to under-powered. The only good player-controlled scenes are the Prologue, Atton/Sion fight, T3 on Nar Shadda and the HK Factory, I also really hate choosing dialogue for your party members, some of the stuff you can say to your sister's as handmaiden on Telos with TSLRCM where simply out of place. I hope you do not do to much of that, especially controlling party members to kill other party members. I personally think that the only time you should control party members is when there is no other solution, like the Atton/Sion fight, where it does not conflict with Atton's personality as you do not choose his dialogue, and you are fighting for something with an ambiguous ending which cannot be with an influence check.
I also hope to god that you do not make the HK/G0T0 confrontation (not fight) player controlled. That would wreck the whole scene. It should simply be:
You bring HK-51s:
You destroy G0T0, and then, after the final Kreia fight, you send Remote an order to destroy the planet/save the planet.
You don't bring the HK-51s:
G0T0 takes control of HK-47, and then, after the final Kreia fight, you try to send Remote an order but it is just static and the planet survives.