I think we should worry about doing match-up numbers and taking match-up numbers to create tier list.
My idea is to take each individual variation and compare it to other Character's variations..take the difference from neutral (If all MU's vs a certain character is 5-5 then the result difference would be zero, 6-4 would be +1 because it is in your favor by 1 match) add them within the variation..do this for the other 2 and find the average
For instance:
Kung Jin's Ancestral variation - Average 0.3
Kung Lao - BS 6-4, HT 5-5, T 5-5 = +1
Kitana - A 4-6, M 4-6, RS 6-4 = -1
Cassie- B 6-4, H 5-5, SO 5-5 = +1
KJ's Bojutsu Variation - Average 2
Kung Lao - BS 5-5, HT 6-4, T 5-5 = +1
Kitana - A 7-3, M 5-5, RS 6-4 = +3
Cassie - B 4-6, H 6-4, SO 6-4 = +2
KJ's Shaolin Variation - Average 0
Kung Lao - BS 4-6, HT 5-5, T 4-6 = -2
Kitana - A 5-5, M 6-4, RS 6-4 = 2
Cassie - B 6-4, H 5-5, SO 4-6 = 0
Kung Jin's overall score - 0.76
Then you take the overall score and put it in order:
Kung Lao - 0.8
KJ - 0.76
Cassie - 0.75
Kitana - 0.68
And that's how you do it, folks.
Obviously this is just an assortment of random numbers to show you what I mean