I'd love if the Vong, the Rakata, and the Sith species were all combined into one civilization/species in the new canon. They build the Star Forge, corrupt the founders of the Sith Order, Revan and Malak turn after discovering them, and then they finally invade after ROTJ.
Yup, Reapers - main antagonists of the game, Rakata - explanation where Star Maps and Star Forge came from. Rakata in KoTOR are more like Protheans in ME. As for TOTJ and KoTOR, I would have loved KoTOR to be more aesthetically similar to TOTJ. It's designs are still original with little influences from original saga (not as bad as Imperial and Republic military in TOR), but looking on some of concept arts made me wish that BioWare did not chose "safe" designs. They have nailed planets but IMHO characters looked too "modern". I always loved these concept arts of Revan and Bastila. Spoiler If someone have not seen it - Revan concept art from TOR. Spoiler Nevertheless, still my best Star Wars experience.
I'd have more respect for the Rakata if they were the main antagonists of the KOTOR franchise. TOR's Sith Empire isn't set up at all in KOTOR I.
Little-known fact: The KOTOR III script was repurposed as John Wick. The Sith would have rued the day they killed Revan's dog.