Even though the ship costumes are still unlocked for people who purchased them earlier, I believe they should be brought back to the C-Store.
First off, I can understand the need to make those fleet ships somewhat more unique in terms of looks, but I also believe that a C-Store skin and a "free" skin that comes with a Fleet ship may function independantly just fine. It would simply give players an option - whether they want a C-Store skin unlock for their ships, or do they want to wait for their fleet to unlock the proper Shipyard Tier.
Second, many ships are obtainable only at very high Shipyard levels, such as the Fleet Advanced Escort. Many people would like to use the Hephaestus skin on their standard AE or MVAE, but now can't, and have to wait months, if not years, just to unlock it for their character (not account...).
Third - the Imperial Costume. It's nowhere to be seen, the shipyard lacks Fleet Assault Cruiser, and even if it were present it would probably be unlockable as late as at Tier 5. Up until then there would be no way for all these Mirror Star Cruiser or Assault Cruiser Refit users to obtain one of the most unique ship costumes in the game, which is disappointing.
I just can't understand Cryptic's move, even from the business perspective. Items from the C-Store are only costumes, while people would still need to purchase Fleet Modules for the proper fleet ship variant. One does not excludes the other. There are many people - myself included - that would gladly purchase certain ship skins now, instead of waiting months/years for their fleet to advance. Seriously Cryptic, these skins are money - you don't want more money?