Vicevirtuoso
The Modetta Man
Separating the great person counters would be an enormous task, as there are dozens of functions that call on the combined counters (as well as the WC resolutions). Any particular reason why you want them separated?
G
Generally speaking, it would help the current poor balance between Great People; specifically, how much weaker Merchants are than Engineers and Scientists. While Merchants will still be weaker with separate counters, adjusting the spawning system to make Merchants not be an active detriment due to the opportunity cost from increasing the time to your next Scientist or Engineer would go a long way towards helping balance them.
More personally speaking, I plan to use this patch as the base for a large mod I am about to start working on, which converts all expended Great People to combat units which have different abilities based off of which type of Great Person created the unit. Having separate GP counters will allow me to balance this much better.