While I have made it clear I don't see the RIFTS system as broken, I do see them ripe for house ruling. One things I don't like is percentile skill systems. I really would like to make it an attribute roll system. Giving attributes a bigger role in the system. I would love going to a 3d6 roll under attribute system for skills. Until then though I think I got a quick fix.
I'm simply going to convert the percentile system into a d20 system. Every 5% is equal to 1 in 20 on a d20. Simply divide the total skill by 5 and round down.
So if a character has a total value in a skill of 45% then he would have a 9 in that skill. A d20 roll is made trying to roll under the skill just like with the percentile system.
My other Idea I'm still toying with is to tun it around and make it a positive modifier and rolling against a target difficulty set by the GM. This one I need to put some more thought and go over the numbers a few times.