One of the things that I've always thought was odd about the Rifts system is the fact that there are three different skill systems. There are percentile skills, resolved on a D100, combat skills, which provide bonuses to d20 rolls, and physical skills, which simply add stat bonuses.
The Palladium system is, at its heart, a D&D-alike (also known as a "fantasy heartbreaker"), which is where it gets the first two skill systems. The physical skills are a completely Palladium innovation. And they make sense, in their own way. Since character stats are rolled completely randomly, the ability to improve a sub-par score at the cost of a skill selection is actually pretty cool. The problem is that there is a tendency for the typical character to be a phys. ed. major: highly trained, but only in physical endeavors. Especially since it takes significant effort for a stat to affect anything in game (bonuses don't start to appear til a stat hits 16, which is very tough to do on a straight 3d6 roll)
This seems to work fine for the game, but it's not very consistent. In order to roll against one skill, you roll one die and want to roll high. Another skill uses another die type and favors low rolls. Another skill isn't used at all and sits on your character sheet once you've added its bonuses.
Another, related, issue is the fact that attributes seem to only exist to provide those bonuses to the 17+ crowd or to meet the requirements for certain OCCs. While the creative GM can find uses for the stats, there's no support for it in the rulebooks.
My proposed solution: Move the entire system to percentile. Skills start at stat + 10%. Stats are rolled using 3d10 (to bring the system fully over to d10s and because the attribute tables in the Rifts books reach up to 30) or via a point buy which produces the same average result.
Fairly short post this month, but next month should make up for it. I'll be talking about levels and advancement and how skills fit into all of that.