Everyone else has their opinions for MK9, so why not throw mine in as well:
1. Considering Armageddon as a "best of" and MK vs DC as a "what if", there hasn't been a game dealing with the MK storyline canon since Deception. This is a great opportunity to take the time to streamline the MK universe a little bit. Over the years, there's been too many twists and turns that over the years created a soap opera level of suspension of disbelief. Johnny Cage is killed! Only he's not (aka they realized how stupid it was to remove one of your main characters because you fell out with the actor who played him). We're going to kill off Liu Kang to make a point that we mean business in this game! Only we really can't keep him dead because he's been the hero of the whole saga and to have him go out like a punk is pretty much the biggest downer possible. Not to mention the whole Cyrax issue. How many times has he been reprogrammed/malfunctioned to switch sides? For that matter, how were a band of ninjas able to master the art of cybernetics? I think it's time to finally end the chapter regarding cyber ninjas. Have Sub-Zero discover the process used to automate them and reverse it. You can even have them not be able to completely return to human form if you like, but no more robots with endless capacity inside their chest cavities. Yes, I realize this is an ironic thing to say considering my username, but if MK9 is going to get back to the roots of the franchise, it's time to say goodbye to robotics.
2. Watching the Fatalities video that came with I believe it was Armageddon for PS2 (collector's edition), one thing that made me shake my head was the discussion of the MK team's least favorite. They all picked Quan Chi's neck stretch and as the worst and all agreed it sucked when they were making the game but they ran out of time. There can't be anything like that in MK9. They're owned by a stable company now, there shouldn't be any rush to push a game out to make any profit they can.
3. No Konquest modes. If they want to make a separate MK RPG, that's fine. To me, there's nothing more irritating than having to go on a Zelda-style quest to unlock items in a fighting game. Don't get me wrong, I have no issue with Konquest modes in and of themselves, they are done very well. Just don't make it so that you are required to slog through it if you don't want to.
4. MK needs to get real. People forget that it wasn't so much the blood and violence that made MK so popular (it was a factor, no doubt), it was how playing the game was like one of those gritty 70s Kung Fu movies that you could control. I tend to notice little things, and one thing that jumps out at me is how Fatalities are presented. In every game from MK II on up, when you perform your finishing move, you get the famous "DUN DUN DUN" fatality music and the move is performed. In MK 1, you had the slower "DUUUUUUN..............DUN" that played through the finisher in it's entirety. It was a slower beat that made whatever being done seem more brutal. Since MK9 will be using the same engine as MK vs DC, there are a lot of places where that "real" feel could be obtained. I even recall playing MK vs DC being surprised that DC allowed their characters to be in some of the situations that played out in the game.
5. Move forward with the story. This kind of ties in with my first point, but I wanted to emphasize it again because one of the things that has always irritated me is how games like Street Fighter will make sequels, but they really take place before or between prior versions of the game. Like I said, it's been 6 years since we've had a canon MK game. It would be great if that much time has passed in the game when MK9 arrives. Let's move past the Dragon King story and have the One Being as the "big bad", lets have Reptile use the years that have passed to find his people and evolve back into a more familiar form rather than completely devolving into a wild animal. Have Raiden be tired of having to be the one to save Earthrealm's ass all the time and be more embittered towards humanity. Above all else, make a rule if someone is killed off, they stay dead. That will make sure no one gets it just for shock value, and let's face it there's definitely some fat that could be cut from the MK roster without causing too much protest. There were 63 people in Armageddon for god's sake.
So I guess to sum up, I'm not saying MK9 should just be a redo of the first MK with Unreal Engine graphics (although that would be cool), what it should be is what Ed and company have been promising us: a return to what MK is all about.