One of my favorite games from the past was "Spaceward Ho!". Similar in a lot of ways to GalCiv, MOO, etc.
GalCiv2 includes basically everything from that game, except for 2 features:
1) Progress bar/line for ships headed to a destination, so you can see the routing, and also the time (I assume this will be in 1.1)
2) "Design cost" vs. build cost for ships. i.e. if you buy a given ship enough times, the cost gets cheaper per unit, and the cost of the FIRST unit of a given type is higher than for subsequent.
#2 could encourage some standardized colony/freighter/etc. ships, not reving the design on every minor improvement in engine tech unless necessary. It would also open up the "export" market for arms -- it would be cheaper for me to mass produce a ship design and trade it to my neighbor for his mass produced design, vs. us each producing our entire navies.
If I were selling ships, I don't think I'd want to necessarily sell them on the doorstep of my main shipyard, but rallypoint them out to some remote location and sell them there. This can be handled through the current UI I guess.