If you look at the access patterns for a dual-core CPU, then one core is always in use a bit more than the other. However, this is due to trainz using one core and windows using the other.
Anyway, shouldn't the CPU driver spread the load evenly through each core?
As for what you are suggesting with regard to percentages, I cannot see a way of implementing it without rewriting the entire OS and any games that you want to use. But, using a 32-bit OS would solve your WOW64 problems.