according to the manual, i would presume that there is something in the engine that determines the best perimeter player legitimately. If this is true, then Man2Man would seem to be the stronger defense against it assuming that you know which position that perimeter player is set to play in during the game. 3-2 would be a semi-defense in the aspect that you can't completely lose if you fail to match up a high OD player against their outside iso player.
Unfortunately, unless i see an opponent that actually runs it, i can't tell A) if there is a significant enough punishment for choosing 3-2 rather than guessing whether or not the other teams uber guard players at PG, SG, or perhaps SF... or B) whether or not the isolation actually determines whether or not player in one position is of higher talent than the other. So it's kinda hard to know.