As a modder always working on creating a bigger, better, longer tech tree (as I always tech rush on gigantic maps and so exhaust the whole thing quickly), one itsy bitsy change I would like to see made is for there to be independent race values for beam, MD, missiles, PD, shields, and armor in addition to the default increases to weapons and defenses for racial abilities. That way I could make a tech like, say, "case hardening" that makes missiles 5% stronger, or "ultra-dense materials" which make armor 5% more resistant and do both without having to include other weapon or armor types in the tech. I'm not saying a new racial ability selector needs to be added for each at the choose abilities screen, just something like Logistics or Miniaturization where it lurks in the background for modders to play with if they want to for their own ends but not necessarily something that will impact a normal game in any way. Though, as it does not impact a normal game in any way, I doubt this change would be priority.
Repair ships would be a good addition, a module that increases by some percentage increases the repair rate of any ships in its fleet at the end of a turn; perhaps an additional use for the constructor module. Likewise, a jumpship would be fun, a module that increases the speed of a fleet by one, two, three, etc. In short, an increased role for support vessels would be nice, instead of the situation at present where support vessels are either TTs that follow the fleet or scouts that poke ahead of it. A reason to integrate non-combat components into combat fleets would make for an interesting depth addition to the gameplay and combat for those who seek it.
Bulkhead component, adds to the HP of a ship it is on rather than the defenses. Cheap, but very space prohibitive.
More spy missions. In addition to sabotaging improvements, I think there should be a variety of missions, such as:
* Sabotaging ships; planting agents to lower the speed, range, weapons, or defenses a ship so long as they are planted there. Blowing the ship up might be fun, but it seems like it would be an extremely cheap method of sniping enemy fleets early on unless that particular mission had a low success rate. 50% chance of the spy reaching an escape pod if you blow up the ship with him on it, allowing you to place it elsewhere, no chance if someone else blows it up.
* Diplomatic missions; infiltrate another race's foreign affairs branch and work to either improve or damage relations between two races. 75% success chance, 20% failure chance, 5% oops chance (has the opposite of intended effect).
* Influence mission; spy goes about promoting products in trade, talks about them a great deal in the media, etc. Doesn't matter the cause, all that matters is it increases influence on that particular planet.
More fun stuff like that to make espionage more interesting.
More to come later if I think of it.