Idea (in General)

well i think that challenge bonus should be based on like your PR or MPR and their PR or MPR

It partially is! =)

well I mean PR or MPR and their MPR or PR.
Right now its your PR vs. their score

That would completely demolish the point of scores.... which I kinda like. :\

No, wait, I was thinking you meant rewards based, not challenge bonus. I'm not sure if that makes a difference to what I said in my first post, but I assume it does.

Challenge Bonus is rewards based, you get higher rewards based on their score vs. your pr.
This is also actually much better in my opinion than your proposed sole pr suggestion for 2 reasons.
The current system promotes you to find the most successful strategies that you can defeat in order to gain a higher bonus which is a challenge in itself.
Secondly, most people fight by score, it's a good indicator of each characters approximite 'real' level (ignoring the fact that some specifically seek out a few that highly inflate their scores). If we were to change the equation to be pr vs. pr then there would just be a flat level (until either you or them trains their exp) where the challenge bonus 'level' would be difficult to set. The new version would make it so you can either get it all of the time or none of the time, very difficult to get anything balanced from it in this scenario.
The only way to get a higher challenge bonus than a mediocre one would be to search for all the teams far higher in pr that have enough wasted experience when facing your team that you are effectively at the same levels.

No Thanks.