You're right on villains. There are plenty that make great possibilities. Even if Kyle Katarn no longer stole the Death Star plans, they could easily work him back into the story with the main part of Dark Forces, battling General Mohc and his Dark Trooper project. Mohc makes an interesting villain because he's not in it for evil, he's in it for honor: he's a Clone Wars vet that became obsessed with personal glory in combat and opposed projects like the Death Star because of it.
I feel like they could have had an interesting perspective flip if they had kept the EU's Imperial remnant but depicted them as the scrappy, ill-equipped fighting force the the Rebels were. Maybe having an element of being "true believers" in the Empire, believing they're fighting to restore order, and maybe even having to take down a New Republic superweapon. Working the Mandalorians into it with an aged Boba Fett in half-digested armor would be cool, too. The idea from the EU that Fett was working for the Hutts in revenge for Jabba's downfall was a good concept.
Xizor I don't think would really work, since his main arc was about attempts to humiliate Vader in front of the Emperor, and unless you significantly developed his character, Steve Perry didn't make him a terribly deep villain. He's fine for Shadows of the Empire but take out Vader's search for Luke and he doesn't have much to do except seduce Leia. And Rey already has a creepy older dude lusting after her.