I mostly kept my older ships. (Still got my original Miranda from the Original STO launch). Others I replaced with Fleet counterparts and say they got a refit. (More item slots, more storage. ) 1-time or reward ships, I'll keep in storage. C-store ships are just placeholders for other C-store ships (for consoles).
Be aware that you can always drop C-Store ships and get them back again since you paid for them. If you do have these and want to dismiss them, make sure to take all the consoles and devices off first otherwise you'll lose these things.
The "free" ships that you get when leveling and lock box ships... all of those cannot be gotten back - you'd have to pay for them again. I'm not sure about mission reward ships (like the Tier 3 Ambassador.) The Tier 5 Ambassador is not being offered anymore so you could not get that one back.
The Rear Admiral ships (the LAST one you get for free) are worth keeping since they are good enough for end-game play. The lower Tier ships aren't powerful enough to do anything serious at end-game (Vice Admiral) because your foes are more powerful.
Personally, I have kept my "Enterprise" ship classes but dismissed my Miranda, Akira... If I need to I might drop my Tier 4 Exploration Cruiser since I have the option to get the higher tier Galaxy.
If they would complete the range of models that you could mount, it would be nice.
Please add Exploration to Star Trek Online! Are you sure it isn't time for a "colourful metaphor"? --Spock in 'The Voyage Home' Star Trek Battles Channel - Play STO more like Star Trek with challenge, teamwork and FUN!
I discard older (free) ships as I outlevel them, and only if I need the slot.
I have yet to buy a ship slot for any character, but there's always a first time
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