I've only played a few of these game series and know about the others mostly through reading, so I didn't understand everything, but this was still a very entertaining read and I wouldn't mind taking part in an RP based in this cross over universe.

696969's suggested quite a few series you might want to include in this universe and I think some are quite good ideas.
DOOM is a fun little series to take ideas from, but it features supernatural elements (i.e. literal demons from hell) that might clash with the mostly sci-fi stuff in this cross over.
Ideas from the Half-Life/Portal universe could be included without too much difficulty if you're familiar with the setting. The actual storyline from the games might have to be put aside because it would clash with the timeline you've already got, but factions like The Combine would probably fit in with your setting.
If you've seen the films, Aliens and Predators would be two species that could be put in the setting without disrupting too much. Predators could be one of the mercenary factions while Aliens could be utilised as bioweapons by any of the factions.
Transformers appear in some of the group shot pictures you've got so they could be fun to put into the universe. Cybertron could be a member of the Citadel Alliance?

In regards to what you've got so far, I'd like to ask a little bit about how Mega Man and Metroid affect the setting. Mega Man (particularly Mega Man X) has quite a few world threatening events in it. Are these just local to Taiwan in your storyline or did they never happen? In regards to Metroid, how much from that universe is canon? Do the metroids themselves exist, or is the Metroid series' involvement limited to Samus running around as a mercenary?