Back when I played SMAC a lot, I found the unbalanced thing was useful for player-vs.-AI games; once I got good enough to reliably beat the AI with the powerful factions, I could play the weaker factions as a challenge. For multiplayer games, though, not so much.

It did, however, make me long for a version of SMAC where you programmed units with AI guidelines rather than control them individually, and where probes could read and alter enemy unit programming.