For a start, I'd name it by battlegroup rather than naming each individual ship, cuts down on the necessity for creativity a little bit (though if the crew wanted to give nicknames, I wouldn't be against that). Endless Space does this, and it makes naming things much easier, I have enough time deciding what class name to give each design.
Battlegroups would be named dependent on their purpose, with historically relevant names like Enterprise and Apollo for the explorer groups, and for the more heavily armed ships we have names like Armageddon, Mars or Tyr. Within the battlegroup, ships are graded and given a secondary designation to go after the group name. The lead ship takes prime, because Armageddon-Prime sounds like an awesome place to command from. Secondaries are labelled with the greek alphabet, because commanding Mars-Omega to fire from your admiral's chair on Mars-Prime would also be awesome. Escorts and other vessels are then numbered, because it's still pretty badass even if you are only torpedo fodder.
The only forseeable problem with this is you either have to lose entire battlegroups at a time, or do a lot of re-naming.
Battlegroups would be named dependent on their purpose, with historically relevant names like Enterprise and Apollo for the explorer groups, and for the more heavily armed ships we have names like Armageddon, Mars or Tyr. Within the battlegroup, ships are graded and given a secondary designation to go after the group name. The lead ship takes prime, because Armageddon-Prime sounds like an awesome place to command from. Secondaries are labelled with the greek alphabet, because commanding Mars-Omega to fire from your admiral's chair on Mars-Prime would also be awesome. Escorts and other vessels are then numbered, because it's still pretty badass even if you are only torpedo fodder.
The only forseeable problem with this is you either have to lose entire battlegroups at a time, or do a lot of re-naming.