I would have hoped they'd make the legendary excelsior better than the Resolute, but it still has the 4/4 weapon loadout and a useless ensign slot. They should have taken the ensign slot and lieutenant slot out and put in another Lt. Commander slot.
There's also the mission accolades in Stranded In Space. The engineering accolade works. The Tactical and Science accolades have been broken for years.
Is your unused boff roster full? The maximum capacity is 15 unused boffs. That's probably why you're getting the message: "Unable to make purchase. please try again later"
Could be specific ships affected. Might want to post a list of which ones you're having trouble with. Every ship I've upgraded has most assuredly unlocked account-wide.