Sounds like all is well, at the moment, regarding wave size and scouting balance, etc.
Regarding the costs of the things like SuperFortress, etc, those are meant to be prohibitive -- it's like building one of those ultra weapons in SupCom, those would take literally an hour and cost everything you had at the END of the game. At the start you had no hope to build them. I've always wanted the Zenith Trader stuff (which is awesome all around) to have a similar sort of balance, that you wouldn't even think of building them in the first couple of hours of the game, because there would simply be no economy for it.
Often it was "I don't have a fortress yet, I don't even have many mark III ships, but I have a SuperFortress that eats every wave that comes to my planet!" and I think that was out of kilter and always was.