I agree that c-store is getting way out of control for a subscription game, the're are items in it that affect gameplay such as efficient BO's and ships with unique abilities.
We used to get extra BO slots with every rank, these were removed from in game at new ranks as soon as they appeared in c-store at per char prices.
The excuse of the additional ship options being available in game is a farce, we used to get 1 free ship per rank and ALL other options were available for in game EC currency at realistic prices. 500 Emblems is not what i would consider being available in game as it would take months of monotonous repetitive missions to acquire this number of emblems without getting any MK xi gear from npc's.
I would not consider $15 or $25 for a ship a micro-transaction for a subscription game and fear that c-store is going to get worse. It is making me seriously reconsider playing STO due to the direction c-store is taking.