Anything can work, but WHY are Tiny Toons characters suddenly showing up in the realm of Mortal Kombat? Are they showing up in earthrealm in a desperate search for help to fight back against an Outworld invasion? Have they taken over the realm conquering duties of Outworld now that Shao Kahn has fallen? There has to be a reason for this other then "I think this would be funny so I made it happen." A crossover still needs to make sense no matter how ludicrous the mash-up.
The more challenging aspect would be forcing your story to stay true to both Tiny Toons and Mortal Kombat. You have to write in such a way that fans of both franchises could get into it, and write it so that events seem plausible in both universes. This, more then anything else is what makes complete crossovers so much more challenging then character crossovers. Your taking two universes with completely different ideals, throwing them into a sandbox, and forcing them to get along as well as they possibly can. It's an incredibly difficult process, as one with experience doing so can attest. I myself find myself taking frequent breaks from writing just so I can figure out how to make the events I'm planning work.
If you can do this, I salute you, and I'll probably read your story as well. But if you just want to write it so Goro can beat up Babs Bunny in a hotel lobby then it's probably not worth doing. If you do decide to write it, let me know. I'll check it out and tell you how you're doing