Checkers is a fun game, but it doesn't tweak my strategy brain cells the way chess does. There's something about the fact that the chess pieces have personality and function that really does something for me.
Lack of flavor in this game has always been a major concern for me and what keeps this game from being great. I know it's got a lot of fans, but I want it to be more. Heck I'd even spend time working on it for free if they'd let me.
But the game feels an awful lot like checkers to me. At each stage of the game you may only have a few varieties of ships in your fleets. Small and medium or medium and large. You have have fighters and frigates, but I'm looking for more of a Battlestar Galactica / Star Trek DS9 feel. The problem is there seems little reason to name individual ships since each one is a clone of 50 more just like it.
In the real navy the big ships are huge multi-year deals and each ship is different from the other because the technology changes. There's also a limited capacity for them due to cost and just not having the trained personnel to man them.
I'm thinking we need the same thing with our space ships. The really big ships in the game should be limited. Each planet should have a ship capacity that's spent on the ships it creates based on the size of the ship. Small ships shouldn't cost anything or very, very little. Big ships (the largest hulls and a few levels down) should cost in terms of your planetary capacity. Each ship could then be named for the planet/region much like Battlestar or Battleships are.
Want to add even more flair -- make the biggest ships multi-planet (in the same system) affairs though this would require rethinking resources and planet interaction.
So in a small map you might have 10-12 of these beasts at your height by the time you've conquered almost all the map. To make this feasible you could have a certain percentage of the cost of these ships free for the first per system.
Want to add even more flair -- tie them to morale. When the named ship from your area does well morale goes up. When it does poorly morale goes down. There's a ton of things you can do with these when there's a sense of emotion behind them.
Given such limited resources you have to think much more strategically than the game currently makes you think. It would benefit you to make them differently to serve different needs much like a chess piece and you wouldn't be so indiscriminant in throwing them away.