I think this kind of thing would go well with...
* having a very large number of units to chose from
* Each unit type having many more and wider spread attributes than a normal RTS
* Some attributes being hidden, and some not. Actually, rather than hidden or not hidden there could be stuff like hidden to the opponent but not the player able to build them, hidden until the unit is tested in actual combat, etc.
* "secret weapon" type units, with extremely high cost per unit and many uncertainties but a slight chance of being gamebreakingly powerful.
* a "rigid attachment" type mechanic, locking multiple units into a single larger structure. Just like you physically glued them together, they wouldn't actually merge into a single unit.
* Special abilities being implemented as stats that are zero or near zero for almost all units.
* Normal distributions for abilities, meaning very rarely would get units with ridiculously high values for somehting.
Also, remember much of normal balancing concerns would be invalid or reversed for somehting like this: just because someone can be dealt a strictly very good or very bad hand doesn't make the game flawed, in fact it can add a dimension to it. What units you can make is just part of the randomized starting conditions rather than a fixed part of the game itself changes the way they are constructed fundamentally.
NINJAEDIT: I got the impression this was more space or naval based(?) so that makes no sense.