Hmmm, usually my end product ship (you're calling yours a stardestroyer) is many many times more expensive than my input ship (you're calling this the barebones ship).
Because my end product ship usually exceeds the input ship by 5 to 10 fold in cost, it would not be possible for me to upgrade from the "barebones" ship to the "stardestroyer" in only 1 to 2 turns (because of the 50% rule). I'd suggest that you should actually exploit this "feature" more, rather than less by increasing the cost differential between your input ships and output ships! Of course the cost to your empire will be that you will definitely need to increase 1) your resource production 2) the amount of resource storage and 3) the number of repair components on either ships or bases to allow the retroseries to work well.
If you really feel that retroseries is imbalanced, then you could cease using it or mod. the required files to make it even more expensive
. I personally find that I need to build up a substantial infrastructure in order to retroseries well, and that this balances everything out (ie. now I've got to spend time building repair ships, more storage facilities, etc.)
just my thoughts,
jimbob