Realistically, having players choices from previous games actually matter is impossible for practical reasons. I think KotOR 2 does a good job of referencing the choices without wasting resources accommodating all the different options.
Having said that, if we are going to continue on as the exile, as I think they should have, you would have to implement some sort of time skip to give time for all your companions to disperse, and have the sith invasion occur without it feeling contrived that it happens exactly as K2 ends.
You can have the exile ditch everyone and go off with T3, HK, and maybe Atton (he can't die without restored content, so he can be included). Mandalore has Mandalore stuff to do. Disciple/Handmaiden, Visas, Mira have Jedi/Sith training to do. You can then say the exile was screwing around looking for Revan for a few years (good excuse to lower the players level and alignment scores). I think that's a decent enough setup that lets old companions show up, but be easily replaceable, sort of like how mass effect worked.
I think the sith invasion does need to occur at some point, for the story to have any stakes, but I'm not sure if it should be at the beginning or the end (for some K4 setup). The story really starts to just turn into mass effect/new Jedi order at this point so I'll stop.