I like to keep my ships around because sometimes I do like to fly them. Luckily, I picked up enough Borg sets prior to the reputation that most of have them. With the idea of "role-playing" on STO, as an earlier blog suggested, it would seem like STO would have addressed limit issues.
I guess my thinking is "Why offer so many ships if we can only have a few?", especially when they keep putting out more ships in special missions, lock boxes, and the lobi store. I would think STO would want us to have them all since they would be making money of them.
I don't exactly do role playing but I've been pushing in my fleet for a pvp event that would be restricted by tier allowing our old ships to get some use.
But I have all the ships I've obtained and never got rid of one. Sure I don't use them but I was working on maxing out the capabilities of every ship I have. I even mounted a spare quad cannons I had on my NX class ship.
Seeing how most ships are now not reclaimable from the store, we tend to keep them instead of throwing them away.
If ships are going to be one shots now, they need to increase the ship slot limit.
I don't rebuild my trays. I lock them then take note in my sto notebook I keep of which officer goes where on what ship and when you change ships set the officers back in their correct slots and your tray rebuilds. I am working on getting enough officers to have one dedicated group for each ship.