DJ Bonebraker
a.k.a Laura
Lately I've built a few Mobile SAM armies, and have had a lot of success with them. I haven't done any tests to see if it is better to have 1 MSAM army or just 4 MSAMs though.
I also built a some unconventional armies in a game a few months ago. I added 1 MI and 1 MSAM to an army with 2 Tanks to see if the SAM would give the army an Air Defense capability. Unfortunently the AI never bombed it and I haven't tried it again since. So I don't know if AA capability is only granted to the army if all the units have it, like amphibious, or if only 1 unit can give the army AA capability.
I do know that most special abilities work, with the possible exception of stealth attack (can't remember if that worked with the Turk army I made in one of the Final Fantasy mod playtests or not) and the definite exception of Hidden nationality...
In the Final Fantasy mod, Cetra Archons can enslave defeated enemies to paladins, Maesters can enslave defeated enemies to Torama (advanced barb unit), and Heavy Tanks (as well as their UU variants such as the Al Bhed Heavy Machina and Orcish Warmachines) as well as Al Bhed Machina Hunters can enslave defeated enemies to Death Machines... When those units are loaded into armies, they still can enslave units.
I don't know about amphibious assault units... I haven't tried making a Marine army yet, but I'll try that out next time I play.