The only way to begin balancing is to decide on an acceptable strength each characters should be at. What I mean by that is to nerf or buff each character until they match the power of a selected character.
For example, we could decide that Liu Kang, Ermac, and Sektor (A tier) are good strength levels for characters to be at. We then nerf and buff everyone else until the selected three are at least comptetively viable or top tier in the new patch.
Otherwise, there will be people who want everyone to be as strong as Kabal, and there will other people who will want everyone to be as strong as Sheeva.