I'd definitely prefer limited ammo. Managing and conserving ammo is part of the fun from my previous experience playing turn based wargames. Limited ammo forces you to think about and make more effiecient firing decisions. With unlimted ammo, you can just fire at anything that moves which is arcadey and really not fun.
However, as you have pointed out, teaching the AI to manage supply effectively may be difficult. I hope you can pull it off though.