Here's the way I see it, 90% of the mechanics are perfect. There are only a few things I would add, some of which might just be doable with current mechanics - but some of it is going to need alterations to the source code, I think.
1) Ship Workshop. Sort of like Alpha Centauri - you can mix and match what componants you have on a classes hardpiont. A vessel can have certain hardpoints (like in SFC3) and differing components will change how the ship behaves in combat.
a) Hull types: fighters, gunships (sfb PFs), corvettes, frigates, destroyers, light cruisers, heavy cruisers, battlecruisers, dreadnaughts, and battleships.
b) each hull type as an iteration: gunship I is the most primitive of the gunships, whereas gunship VI is the most advanced.
c) each hull type (and iteration) has a certain number of slots for differing systems
d) slots
i) there are several types of slots: primary weapons, secondary weapons, tertiary weapons, engines, hull systems, and more
ii) weapons increase attack power (or defensive power in certain cases, like the Plasma-D)
iii) shields increase hitpoints
iv) armor, sensors, and engines increase defense
vi) warp engines increases speed on the game map
vii) sensors also help detect cloaked vessels, etc.
e) designs should be savable
f) once you research a better component you should be able to upgrade the component on a vessel thats already in the field (if its in a system that has a drydock). However, you should not be able to upgrade a Lightcruiser I to a Lightcruiser II (unless you have a specialized research; which should be different for each hull and for each upgrade)
2) Characters
a) characters should be able to gain experience and have there skills get better
b) a character can be assigned to a ship or a system and when they are at such a place, their skills improve the effect of the unit (or fleet if there skill is high enough) that they are assigned to.
3) Renaming of units (You should be able to call a specific Heavy Cruiser the "USS Enterprise")
Obviously the biggest thing is the Starship Workshop. I'm fairly certain that the characters can be done inside the existing engine. The renaming thing I'm not so sure on.