About the fighters in each organization: Fair point. I accept it. 
TV deals: I agree with you, and that's why it seems to me that JF should score a point. They had a national tv deal for most of their events, and an international deal for 70% of them.
Fight Matrix: By your criteria, only UFC would get any points. Here is the breakdown of the top-10 in all divisions, per organization: 
Heavyweight: 10/10 - UFC / Strikeforce
Light Heavyweight: 10/10 - UFC
Middleweight: 9/10 - UFC / Strikeforce; 1 KSW
Weltherweight: 10/10 - UFC / Strikeforce
Lightweight: 8/10 UFC / Strikeforce; 2 Bellator
Featherweight: 7/10 UFC; 1 Dream; 2 Bellator
Banthamweight: 6/10 UFC; 1 Dream; 1 Bellator; 1 Shooto Americas; 1 Bellator / Shooto Americas
Flyweight: 7/10 UFC; 1 Pancrase; 1 Legacy Promotions; 1 Legacy Promotions / Championship Fighting Alliance
Out of 80 guys, 67 are fighting in UFC / Strikeforce. Bellator ranks second with five guys, which is not even 10%. UFC's dominance is so great that, for the rankings to be of any value to determine notability, we need to take into account the number of fighters, not the percentage of them. We should also look at the rankings up to the top-20 or top-25.