Oh good. I woke up just in time for more Gundam talk.
No need to keep up that facade; we all know you love it, really. :3
so would you say that using one or the other would depend on the situation?
Pretty much.
Zaku II is clearly more melee-oriented with those abilities, and the Commander is more support-oriented.
Also, the Zaku II is only a C-rank (only gives 2 points on death) while the Commander is a B-rank (3 points on death), so depending on the room, you may not be allowed to use one or the other anyway.
I would mention the rock-paper-scissors aspect, too, but the Korean version of the game is removing that so I can't see it being around in the NA version much longer, either.