I find that smac had some serious balance problems, like the fact that you could create units without armor which were absurdly cheap, and just plan tactics so you'd never be caught on the defensive. Even if you chose to use armour, it was globally weaker than weaponry anyway, so defending was usually a losing situation and it wasn't worth the chance at survival, versus the extra cost for building that unit..
The unit workshop is a pretty neat concept, but fundamental flaws like that would need sorting before it could be considered. And in any case, it would be an excessive amount of work for very little gain. I'm not sure modular art is even possible in the civ engine, so you may never get things represented on units without creating an unfeasibly large number of variation models to account for every possible combination.
The promotion system works pretty well, although I'm not keen on the implementation of increased support costs, rather than increased build costs, for using abilites. I'd personally rather see a one time credit cost attached to taking an ability, rather than constant maintenance.