Example, on turn 1, with just the starting tech, you can design a new unit that will be a LOT better than the starting "basic guard". Granted the better unit will take longer to build, but it will have the same maintenance cost, so the economics only make sense to bypass the built-in units, and always make your own.
I think that would be a pain, so I vote for good-enough built-on units so we don't have to build all our own. Personally, I got tired of designing ships in GalCiv2.
I might get a lot a hatred for this, but I think they could have gotten along fine without any design-your-own for ordinary troops. I know it is traditional in space games, but a swords and magic game will probably end up more hero-centric, and we will want to spend our time leveling-up our heroes and getting better artifacts for them instead of re-designing our cannon-fodder every time we get a new tech.
MOM and the Total War series did fine with built-in units, and games like RTW & MTW got a lot of replay value from the differences in the fixed units available to each faction (Greek phalanx inf vs Parthian horse-archers vs Carthaginian elephants, etc). In GalCiv2, despite (or because of) the fancy ship-design capabilities, I ended up with pretty much the same ships, fighting the same way, no matter faction I played.
With or without design-your-own, I would like REAL differences in the troop types available to various factions. One with good cav but crappy infantry, one with good armor but weak offense, etc, etc.