Eh, I think they'd have to come up with something completely different to really make it work, though. Sure, they could create a different but similar religious nut faction, and a different but similar researcher faction, and different but similar mind worms, but I just don't think it'd work out very well with that kind of "let's copy this thing that was awesome, but tweak it slightly" attitude.
I wouldn't
really want to play a game where everything was the same but slightly tweaked, but let's be fair: The factions aren't ultra-compact packages that you absolutely can't take anything away from. If you understand what concepts about the original factions are fundamental and what are more about flavor, I think you
could simply replace the flavour and come out with something that's better than the original in an absolute sense. Let's have a look at the factions in roughly descending order of "copyability", i.e. roughly how similarly a faction has to be designed to its SMAC version to conceptually work:
Morganites: Capitalists. Replaceable with more capitalists. As long as you aren't so lazy as to put in "Americans" and call it a night, you can't really go wrong with any flavour. Well, don't put in "Japanese" either, unless you're out to appeal to players with eighties nostalgia.
University: They're the faction that's for science. FOR SCIENCE ALWAYS FOR SCIENCE ABOUT EVERYTHING! The Cold War stereotype is entirely interchangeable with any other vaguely science-oriented one you could think of. Modernised versions of hard-assed German doktors wearing round-lens spectacles and using the underclass as test subjects, Chinese with a burgeoning bureaucracy where no-one even knows about any lack of ethics (or, never finds out about it through official channels anyway), etc.. Or, since the University made more use of the national stereotype than the other factions, just have them be an international league of mad scientists led by a Doctor Evil.
Peacekeepers: Look at your other factions, pick a nationality that isn't represented, make a leader out of a Kofi Annan substitute from the chosen nationality, done.
Gaians: Perhaps the most inevitable faction in the game. Sort of difficult to replace because of that. I guess one thing you could do is split them into two, ala Gaians/Planet Cult, but along a different axis. For instance one unscrupulous (and very secular) faction that deliberately uses the Planet as its attack dog, versus a more mystical and peaceful one. A hybridisation faction vs. an all-native ecology (with the occasional greenhouse for humans to grow food in that won't blow their heads up). Etc..
Spartans: Getting tougher now. The Spartans would laugh the Tea Partiers out of the room. I'd personally redesign them as based more on an ideology similar to national romanticism - including an almost fanatic appreciation of old "great" art - but without any one nation as the subject. Sort of a "we humans have fighting spirit" thing. Given that we probably won't have a SMAC II until, eh, 2200 or so, they could even idolise Hitler and Stalin :p
Believers: Miriam's really the hardest leader to figure out, and I love her for it. Is she the simple religious fanatic she plays like? A compassionate Christian whose aggression value just happened to be fat-fingered by the developers? A charlatan abusing the faith of her flock? Is she really a pretty reasonable person during the midgame, until the development of the really humanity-changing endgame techs makes her go nuts (as some of her quotes would indicate)?
Hive: The Hive's a beautiful, beautiful faction. Totalitarianism, repression of the very human spirit, defeating its enemies with human wave tactics... with everything led by a
frighteningly intelligent, soft-spoken, charismatic man with some very interesting ideals. I got the conception from the game that if Yang just had an hour or two to discuss the subject, he'd have no problem convincing you that everything the Hive does is really for the best and the other factions really should just follow suit. The leader's nationality improves the initial facade of "evil commie", even. I can't think of anything you could replace in the Hive design without breaking it horribly.