I could only guess you mean MFCTI...
I tested it some time ago (6 months or something) and I remember that I was very limited. I could only manage a little amount of groups (6, if I remember right) and I could only give them basic commands (like "take that city").
Operation Flashpoint: Commander offers much more freedom! You can basicly create unlimited groups (63 groups is the limit of OFP, soo no more than that) and order them to move to any point of the map.
As I've never played MFCTI again, things might have changed, but I really think OFP:Commander differs in many ways!