Well it seems that if you can pilot one mobile suit, you shouldn't have that much trouble adapting to another, including from Federation to Zeon mobile suits. GMs are not equipped with the Core Block System, however.
Depending upon how immersive you would want the world some things would change gameplay.... I review which gundam series I have and make some notations to post here later.
1:OS for the various factions would differ unless the mecha all come from one solitary manufacturer i.e. Patlabor
2: Cockpit layout like American and European vehicles may have the layout differently
3:Security afterall we are talking a military mecha would most likely require an encryption keycard and password to start the unit
Well, some shows feature biometrics as a security feature for the mecha (example is the Gundams of "Gundam 00"--at the very least they do an eye scan when activating). A couple feature something about how they only work for a certain type of people/race/whatever because of reasons like not having a brain that can process whatever the mecha is showing you fast enough or the mecha's reflexes being calibrated to a type of reaction speed that not everybody has.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.