Regarding game balance, I don't have any suggestions as of yet.
More units would certainly be good, a bomber sounds like a great suggestion, maybe various types of privateer ships and a whole range of pirate ships.
Maybe when you research a certain military organization or construction tech, you can build a national wonder [only one per 'era'] that would add a certain flavor to your units. Say you've already expanded quickly, so you want a more defensive fleet, you build the 'applied x theory of shipbuilding' national wonder and all of your ships until the next major tech are all slower but have sufficient defensive capabilities to compensate.
This method of shipbuilding would not only allow for something to replace all the unique ships that the scenario doesn't have, it would allow greater choice and flavor to forces [and give unit graphics people something to have fun toying around with]. There would be a researchable theory for each 'stage' of the game, possibly each one more powerful than the last
Theory ideas:
Defensive theory
Hit and run [pirate?] theory
Bombardment [long range?] theory
Meat-grinder theory [assault] theory
Special weapon theory [lots of unique abilities]
Divine wind theory [IE desperate suicide attacks]
I would like to see a great number of random events in whatever Final Frontier Mod, humans are prone to error, but hyper advanced technology handled by humans is even more prone to amusing outcomes.