cogadh: I wouldn't expect FleetOps to be included at all. While the community considers it "essential", since multiplayer won't work without it and it does fix several bugs (plus add some features), GOG's version likely wont include it, mainly because it doesn't work with the single player game (works with "instant action" not the story). GOG's version will simply be packaged with the official patches and a wrapper like DXwrapper or the previously mentioned dgVoodoo, which will allow the game to run, minus the multiplayer (GameSpy), in its completely "vanilla" state. I'm sure FleetOps will still work with the GOG version, for those that want to add it to the game, though the FleetOps guys might need to first do some updates to it to account for any differences in the GOG version (honestly there shouldn't be any major differences).
Yeah that appears to be the case. So far for me it runs great. It would be useful at some point to get a guide stickied in here to get fleet operations easily set up so more casual people can get in on that.
Likely very easy to copy your game directory and patch one, use the other for campaign.