This sounds interesting I hope there are twice the available Mercenaries in the game, I also hope there is a way to select what mercenaries will be in the game. One additional thought is to have each level mercenary only available at different Bazaar's for instance one Bazaar maybe only has the first tier, another may have the third, ect... Last suggestion add on a fourth tier for late game and, need to be able to upgrade Mercenaries. Maybe not like you upgrade ships, maybe have to visit the bazaar again and he will offer and upgrade for x durantium + thulium and $$ and this ship gets x. Allow one use ships to be upgraded to be multi use ships as long as they are upgraded prior to use, although as a player you take the risk of loosing that ship in battle if your sitting on it as that multi use ship may cost too much right now to upgrade it. One could even have to fly the mercenary ship to the upgrade bazaar to even get that option...
This would put a nice additional feature on the mercenaries.