I would attempt to have a more "full" experience with sort of a regression in the series. I am going to assume that WB ISN'T impacting my ability to change things.
1) I would opt for removal of the modifiers in the towers of time and instead focus on a new mode -- whether it is some form of tag team fighting, create a fighter, etc
2) I'd make a coherent, fully fleshed out story WITHOUT chapters instead it would be single fights, with story behind it instead of following one character
3) I'd make the majority of the system regress; although a somewhat hot topic, I think that the game should be heavy-combo based. I'd keep krushing blows, but all of them would lead to COMBOS. Of course there are zoners and mid range characters, but the bulk of characters do combos. I say this because it's one of my favorite things in fighting games
4) I would have a creative way(similar to soul calibur) of editting outfits for characters. You could also make your own dream fighter that uses the fighting abilities of a certain selected character. This way, Jacqui can be made a skin for jax, for example.
5) I'd remove fatal blows or super attacks and instead add 1-2 more fatalities per character
6) The Krypt would be set in stone, all one currency (coins) and all it is are custom parts for creation mode
7) I'd remove variations, have characters with glaring weaknesses and extreme strengths
8) I'd keep Kombat League, have filters for wifi, remove rewards and instead put in leaderboards and recognitions of character mastery (like Skarlet mastery level 10 would be the highest or something)