I remember that mission. It has a few of those commando's in the plane and the others fall down with you. If you play on normal or hardcore mode those suckers take forever to kill. It's perfectly understandable you don't kill more than 25 of them in that mission. This is also the only mission where Stag commando's pop up. Chances you'll find them anywhere else in the game are nearly non existent unless you increase your notoriety to 4-5. Most people will be using a tank to last long enough and they'll probably have a homie controlling the secondary turret which shoots the (rare) VTOL carrying them. Killing commando's is not something you do automatically by just playing the game. Stag commando's do not spawn on the ground like others. It's like the morning star specialists, they only spawn in an aircraft and only at notoriety 4 and higher. Seriously if you're claiming you killd 25 commando's during the air steelport mission then that's a mean feat. I've played that mission several times on PS3 and the plane as about 13 of them to shoot, but you'll probably won't kill them all because the last few appear when your timer starts. After that a whole bunch of them fall down the plane with you, but I never got the main gun to actually hit them. I saw a vid somewhere where the rectangle is right on the enemy and the main gun shoots and hits. Well that doesn't happen for me. It goes wide over, so you're stuck with the machine gun. So you kill a couple of them, but you'll mostly be focussing on getting the tanks destroyed.
Actually, in my experience, a couple of commandos appear in one of the missions before Air Steelport - I think it's during the latter half of My Name Is Cyrus Temple, but don't quote me on that!. I don't tend to get any from high notoriety, because I usually zoom through the Stag missions without 'partying' with them too much, as trying to survive laser beams does my nut in, especially if I'm in a 'jacked car. But every time I've played through I've had the commando kill counter sitting at 2 going into that mission... well except maybe the first time, as I didn't know to pay attention to it at that point.
13 on the plane sounds right, though, and I'll concede that it is really hard to clear all of them once the timer starts - I've managed it once on normal, but I had the good fortune to take 4 of them out quickly, with a well placed grenade... unusually for me!
IIRC around half of them appear before the countdown starts though, and you should have a decent enough weapon to pick off at least a couple more whilst making your way to the tank before the timer runs out, even on hardcore. The real nitty, gritty does come once you're falling in the tank, though.
I usually play on normal, but I have done it on hardcore as well. However, I can understand where you're coming from about the main gun. My first playthrough was on casual and I resorted to taking them out with the machine gun because I got the hang of aiming that weapon much quicker. On subsequent plays, after I'd turned up difficulty, I realised that you could take out small groups with the explosion from the main gun's shells. I probably only hit about 50% of the time now, but if you target one in the middle of a group you can usually get 3 or more at a time, saving the machine gun to pick off isolated ones.
It did take me a little practice, but I honestly had no idea it was a common issue. I dunno if there's some trick I'm using to aim it right... it's certainly not something I'm consiously aware of. I'll try paying closer attention next time I play the mission and see if I can figure out any tips to post.
As for homies, I very rarely use them outside of missions and activities where I'm forced to. In my experience, they just get in the way, either by dying all the fraggin' time or, like your example, by being kill stealing 'tards!