1) Argoseyer: If you can't use any given element, eliminate it or it's dead weight. The Phase Bubble is immensely damaging even for those who are not skilled with it, especially on Destroy the Base missions, so it's worth keeping around... on a mounting point, if you've the skill not to destroy it when doing so. However, she was utterly incapable of using the Beam Tendrils, so those were removed and replaced with whatever the heck else I wanted. Yes, interception is good, but when you're twenty times better with a Point Laser, it's best to swap them out. Granted, I felt bad about it, but I also wanted to put the thing to maximum use, so I just got it over with and moved on.
My current character is deliberately customized around the Argoseyer in preparation for getting it, so this obviously won't be a problem.
2) Gladius: Depending on what you want it for, it can be fairly practical to break its legs and turn it into the nastiest Harpy known to man. To me, it's just a powerful machine, one which can be altered to your heart's content. Although I felt bad about taking the Beam Tendrils out of the Argoseyer, this mecha was mine, and its history wasn't so spectacular. I felt I could do what I wanted with it.
3) What the hell is an Anubis?