Yeah the green beret being the only one who could carry bodies can be a real pain. The lack of a silent kill/KO for most of the other characters can be a problem too. I guess you could say it makes things more challenging,as if the game wasn't hard enough already.
Thats why I love C2 so much, it fixes all the issues with the original as well as introducing lots of new features and having some great missions. C3 just didn't take the series anywhere new so was pretty poor in comparison.
Have you played the 4th, the FPS one? The demo was enough for me, its not a commandos game afaik just MOH with different accents.
I've still have never played the add-on, I will do once I finish the original. I only bought them a few months ago- the first time I played it I borrowed it from a friend.