Ah, a pacifist invasion, all of the conquest and glory, none of the blood and guilt.  It may come to that some day, but not yet.  Underneath all the gags and shiny equipment, GalCiv has this truth: people dying, slaughtered in senseless numbers, is what war is all about.   Otherwise, it is just chess with exploding pieces. 

More than just a game mechanic, that truth should stay there at the core.

(Gotta agree about the Iron Giant reference, love that one.)

Fighting with 'real viruses' has been around for millenia. People have been throwing dead stuff over the walls of besieged cities in the hopes of spreading disease and illness since at least the Classical period, and in more modern times have devised more effective ailments and delivery mechanisms, though employing such a weapon is currently illegal. Fighting with corrosive gas has been around since at least World War One, and is currently considered illegal. Fighting with drones is already a part of standard military operations. Fighting with computer viruses is most likely already being done. How exactly is any of this stuff 'coming soon but the later bit would be a few more years from now'? All of it has already been done or is currently being done.

As far as mecha go - if there's a logical and reasonable justification for why the vehicle took the form it did, then I'm okay with it. However, I would point out that a choice between 'fighters' and 'mecha' is like a choice between mounting missiles or having pink ships. 'Mecha,' to my understanding, refers to the form a vehicle takes rather than to its role in combat, whereas 'fighter' refers to a specific combat role. As such, aside from fairly significant concerns about the practicality and effectiveness of such a design choice, I see no reason why a specific vehicle could not be both a fighter and a mecha.

I am not in favor of mechs in a universe not centrered around their existence. The reason being that machs make no military sense whatsoever in any battlespace: land-sea-air-Space. In Space a fighter will be faster, more heavily armed, it should be able to turn on a dime - the only limitation being g-forces and some kind of inertial compensator could solve that. On land the the development of powerful weapons means that being small difficult to hit is vastly preferable to size - even main battle tanks are constructed to minimize their profile, at sea armour lost its relevance with the advent of modern missiles as it is impossible to apply armor in such a way to offer protection - much better to avoid being hit. A huge warmachine is going to get shelled, missiled or TAC-nuked in short order, and the loss of such a unit would be very costly 

 I think that the assumption should be, at least for Space combat, that the very first weapons should be equivalent to thermo-nuclaer weapons in the megaton range - as the tech for developing such weapons is exstremely simple compared to FLT artificial gravity etc.

In short, big*** robots, tanks etc are awesome, cool and very entertaining - but also very very silly from a miltary perspective. And from my perspective at least GALCIV is a bit too "hard-core SCI-FI" for that to fit in.