I'd like to see more Trade Goods, especially ones that are unique to races. I'd like to see the Galactic Guide Book be a trade good, if nothing else.

Some randomization in what tiles will be able to be Teraform-able on planets. Some have more tiles, some have less. Or at least more consistent final-PQ numbers for lower class planets. Right now, fully teraformed class 4 worlds end up with more tiles than fully teraformed Class 5, 6, or 7 planets.
Bonus tiles can sometimes be tiles that have to be teraformed.
More attributes that modders can get a lot of use out of:
Alternate-Attributes for things other than Ship Components, and for other attributes than just Cost. Being able to trigger these alternate attributes via tech requirements would be nice too.
Multiple Tech Requirements for Planetary Improvements, Ship Components, etc. This can already kinda be done with Starbase Modules (ie: Smart Drones is a prereq for a later Economy module, so that module (and the later ones) effectively require Advanced Computer as well as whatever tech they come from. Multiple tech requirements for techs already exist too, but they don't display properly, sadly.
A placement limit tag for Ship Components. A way to specify a group of modules that you can only have so many out of that group on a ship would be nice (kinda like many of the Advanced Modules currently work).
Speaking of Advanced Modules... more of those things with different effects would be nice too