Personally I wouldn't go changing anything in Wayfarer/RQII combat system. (Clarify, certainly.) Combat maneuvres and hit locations are what make this game so special, and if you go changing it, it will become just another d100 and would make me wonder why bother? BRP is already doing the simple version of d100, I see no sense in trying competing with it, as it has a head-start in this. The appeal of Wayfarer should be in its unique, deadly and realistic combat system. IMHO of course.
It is the magic system I am not so sure about. The current system offers an interesting mix, but I wonder if this is too Runequest and rune centred for generic use? I've been trying to think how to bring the RQII magic system somewhat closer to generic high-magic system, ala. D&D 3.x, and I see some minor difficulties in this area. On the other hand the magic system is very interesting and versatile, so I don't want to dumb it down too much. Any thoughts on this?