I know someone said this before, so I am not gonna pretend it's my idea, but................
a judge on each side of the ring and give the ref a say as well, so you get 5 scores.

Make it mandatory that the different sanctioning groups have their champions fight each other.
Let's be honest the alphabet isn't goin anywhere.

defenses would go for say IBF

Champion vs.

1) Mandatory (IBF)

2) someone else in the top 5 on their sanctioning group (IBF)

3) A different sanctioning groups champion (WBO)

4) Mandatory (IBF)

5) Mandatory in new sanctioning group (WBO)

6) A different sanctioning groups champion (WBC)

7) mandatory (IBF)

mandatory in 2nd sanctioning group (WBO)

9) mandatory in 3rd sanctioning group (WBC)

10) Final Sanctioning group champion. (WBA)

At this point we would have a clearly defined champion for each weight class.

I also think that anyone ranked in the top 10 should be required to fight 3 times a year

1) free contract.

2) someone ranked up to 5 places higher.

3) someone ranked down to 5 places lower.