I don't think we need more than just helmets and body armor visible. Those two are essential, in my opinion, for any 3rd person, top-down, tactical, what have you games. It creates a bigger attachment for the unit in question when they look like they have some good gear on and makes me care for them more when I can suit my favourites in the better looking or the best armor. It also adds to the immersion. I mean, imagine playing the new X-COM games without ever having different looking armor on your soldiers. That would be pretty bland. It'll be disappointing if there's no visible equipment at all beyond guns and gadgets, or if there's no way to customise your mercs from their default looks. In a game like JA where the mercs are the heart and soul of the game one would expect to see something you can change on them.
How about this then: The game currently has no custom merc option and by the sound of it it's probably unlikely to happen. This would be the perfect opportunity to introduce your own merc into the game who would get all those fancy helmets and gear shown on their body, making it your very own, special looking bad-ass without having to "ruin" the aesthetics of the established characters. Hell, if there turns out to be no way to customise any of the hirable mercs, then you could go nuts with the custom guy and make him all kinds of action hero type looking during the character creation if nothing else.