There are a lot of options here, more than they've ever had before. Here's what I think about a few of the obvious ones and a few not-so-obvious ones.

Shang Tsung - Can't go wrong with old reliable. Wouldn't be hard from a storyline perspective...if Raiden's energies "reformed" after he sacrificed himself, there's no reason a few dozen evil souls couldn't bring back Tsung. I do think they should "upgrade" him or something though so he seems like more of a threat. Bringing back the morphs couldn't hurt either, and they'd probably look pretty sweet on the next gen systems

Quan Chi - Not a personal favorite of mine but still a heavy-enough hitter to warrant the spot of head bad guy. Not sure how they could get out of his "death" from a storyline perspective but I'm sure they could come up with something.

Dragon King - He really seemed like a one-off character to me. I doubt he'll be back, as the giant monster position is usually reserved for the "guardian of the boss" position instead of the main bad guy. I enjoy MK:D as a game, but I really dislike how in the opening cinema their three heaviest hitters they have COMBINED can't even phase him....but then in the game someone like Li Mei can singlehandedly kill him and make him explode into oblivion. Just doesn't make sense to me.

Goro - Disregarding what I said just a moment ago about the huge beast usually being the guardian of the real boss, this could be pretty interesting. Someone/someones resurrect him, he goes nuts and kills the people who brought him back. The now power-enhanced Goro is pissed that he died as a result of joining forces with Kitana, feels let down by her, and returns to the evil side of things. He tears through the tournament to become champion again, and now needs to be stopped.

Shinnok - I know a lot of people hate him, but I think that's partially because he was the head villian in what is pretty universally regarded as the most lackluster game in the series. With the right storyline I think he could work. Now that Quan Chi is "dead" the amulet could fall back in his hands.

Ermac - Stop laughing! Well...ok, laugh a little. But hey, Reptile is supposedly the vessel for the Dragon King, so you never know. Anyway, Ermac's power goes nuts and starts sucking up every soul in sight, like a psychotic, out-of-control Shang Tsung. They could certainly augment his look to reflect this and he could make a decent bad guy. That name isn't too threatening, but maybe they could rename him or something.

"Evil" Raiden - I'm not calling him evil, it actually says that in MK:D at some point. To me it's just pissed-off-but-justifiably-so Raiden. He wouldn't have to be some Shao Khan/Dragon King-esque "control everything and kill everyone" villain, but maybe a god who is both frustrated and angry with humanity and wants to merge the realm with Orderrealm to keep people from fking up like Shunjinko did when he brought back the Dragon King. This is actually probably my second favorite choice, next to...

Shao Khan - MK7's opening cinema....I want (preferably) Quan Chi or maybe Shang Tsung alone in a room, making some crazy plot to take over Earth/Edenia/etc...when a shadow falls over them. They look up with a look of terror on their face, and a familiar sledgehammer smashes the shit out of them. More simple and to the point than the previous intros, but it would be cool as hell. He's been away for a while now, it's time to bring him back. I know he's "dead," but you know damn well that no one ever stays dead in the MK universe (someone even mentioned that on the MK:D bonus disc). Hell, I just want to hear him as the announcer voice again, that is, if Steve Ritchie is still in contact with Midway. Anyway, that's my favorite option. Unless of course they combine the last two and go with...

"Deadlier" Alliance - Obviously they wouldn't use that cheesy name, but it would be an interesting concept. Raiden meets with Shao Khan in the afterlife/Netherrealm/whatever and come to an agreement where they sort of "meet in the middle" on their ideaologies. "The realms must be under our control but it doesn't mean murder and enslavement," that kind of thing. This option would also make it so Raiden isn't just another character and could be given the power a god should have. It's always bugged me that the fking god of thunder and lightning is on the same level as Sonya and Johnny Cage.

Anyway, if anyone has any other ideas or comments, go nuts. *Edit* - By the way, try to keep the spoilers to a minimum here if you've seen the endings of a lot of MK:D characters. I know some character endings might seem like it's going to go in some direction for the next game, but there is a ton of stuff from the end of MK:DA that isn't cannon (Kano being inhabited by Kang's soul, etc). Plus I've only beat it with like 5 characters so far since I haven't had a lot of time to play it