RMSS also has about twice the number of development points than RMC has. So you would have to adjust them.
As for the skills themselves, RMC averages stats while RMSS adds them, so the RMSS stat bonuses are smaller. You best bet there is to just add a stat to most skills to make sure each has 3 stats that can easily be added together (either that or change the stat bonuses to be RMC-like and average them -- I prefer the additive method myself).
Another issue to watch out for is the O/E/R skills, you will either have to ditch them or change how they work (personally, I would suggest changing the DP costs for the skills accordingly (i.e. divide by 3, rounded up; divide by 2, rounded up; and double).
Other than those issues, swapping out the skill system should be a snap (since the skill system is the largest difference between them).