So, there's talk of the new duty roster system and the idea of upgrading old ships as you level progress.
What I was thinking was that in a new system, you could swap out duty officers for bridge officers. Maybe 5 duty officers = 1 bridge officer, or 10 if you wanted to go up a promotion slot for the bridge officer. This way, it would have some sort of detrimental effect on those who wanted more powers for their ship. Also, since duty officers will probably work much like BOs where as you level up, you get better ones, the trade-off will eventually get more and more severe.
There would still be obvious limitations depending on level as to how many BOs you could have and then there would have to be some sort of retrofit at the VA point to deal with the reasons why Captain level star-ships now have the extra BO's and BO powers while maintaining all of their previous crew.
Also, on a side note, this could bring more diversity in the long run to the retrofit star ships as you might could use your token to upgrade an old ship. You may not have design specific abilities given like the saucer separation, cloak, multi vector, or shielding, however, you might get something retrofitted to your ship to make it interesting.
Oh, I forgot to include! The idea is so that ship crews stay at a finite level, and that way a MIranda class is still a MIranda class even upgraded to RA 5, but the Miranda class might be Captained by an Admiral now who has re-equipped the ship, retrofited it to carry a few more weapons and a bit better power out-put, and changed the crew roster to include only his best men.