Yes, well, we can't have no more of those 45-degree points. They're just too unclassy.
Also, yes, get the story first thing. The title can wait until last, or can be something supersimple like "Fybertech". As for the backgrounds, I would just suggest you just edit some mega man backgrounds to make them look less cartoony and more utilitarian. I can help you here, I've got a few edited backgrounds from that old comic I tried to make. Also check
http://www.sprites-inc.co.uk/, they have some choice bits that can't be found on vgmaps.
AS FOR THE COMIC SIZE, this really doesn't matter too much. Whatever you think will give you enough room to fit everything you need. I'd suggest the old hazlabs standard of 250x150, but if you really need space, you could probably bump it up to 300x200.
Also, if you're going to put all those people in there, you'd better make sure we all have pretty similar sprites, or else it'll be a disaster. If you were going to use those big tall sprites Boris made, I would suggest 1) that you make them shorter, or 2) that you make the frame a little bit bigger to accommodate them.
Back to the story, I think it would be a good idea to just start off with Fyber, add Boris, then Vito, and then find different ways to introduce everybody else. This could be just an exposition comic, and then whatever story arc you wanted to go after could be a completely separate comic.
O-okay, I'm d-d-done-
* Prox starts gasping for breath