1: Allow multiple instances of certain building types on single planets. This would go a long way towards specialization and putting an emphasis on trade between colonies, in particular food production, mining and industry. That way you're one terran/water world can have multiple farms that export food to your metallic planet colonies that can't grow any at all, but are rich in mineral wealth.
2: Specialized industry types. These should be in addition to, not a replacement of, existing general purpose industry blocks. For example, a type that only produces supplies, but lots of them. Or a drug manufacturing center. Right now we have the fuel production center but that's the only real specialist industry so far.
3: Manual AI fleet creation option. Right now colonies, while expensive to set up, generate obscene amount of money once they get going. Right now ship build orders exist in two different worlds: manual orders for your own personal use, and a priorities box system for creating AI fleets. I propose an option (selected at new game start only) to merge these two into a single system wherein the player manually orders all ship construction and no AI fleets get automatically built at all. Instead, in this mode, any ships in player storage can be assembled into AI fleets that will then patrol in an area dictated by their military base size. This would make an excellent money sink, obviously, and give players much more control over what they send into the field. It also gives a good place to get rid of surplus ships besides just selling them outright. When the situation is dire enough, just press captured enemy ships into service into your own fleets.
Also manual control over at least the creation of merchants would be nice as well, and give players more reason to actually invest in those ship types. See also "Distant Worlds" when playing as a pirate faction.
4: More military base types. This would require new planet siege mechanics, but I feel it would be worth it. In addition to the general purpose types we have now, have bases that specialize in producing (training) crew, marines, orbital defense or pure fleet coordination. Also, instead of the planetary shield generator being a flat defense bonus, have it instead be a system that stalls an enemy fleet in orbit for a certain amount of time so that you or your AI fleets have more time to intercept them. Orbital defense should just straight up inflict damage on attacking ships, depending on their level.
5: Overhaul AI Cores & Bonus Devices. An AI core should be more than just something that gives +1 to anything you stick it into. They are, after all, learning machines and as such they should be treated more as little NPCs rather than mere items. By this I mean that an AI grades should act as skill caps and that they should level up over time just like organics. When placed in a planetary role they will slowly but surely learn to specialize in helping whatever facility that they are in. This would be easiest to explain with examples...
Example A: Player finds a Gamma level core, with a max level of 5. They decide to plug into a planet's farming slot. Since it starts off as level 1, it gives +1 to farming. As time goes on it gets better at this, eventually working it's way up to +5 worth of bonuses. Things such as production and cost reduction are now skills that are selected when an AI levels up, same as with NPC assistants. Doing this, the player decides to allocate +3 to food output and +2 to overhead reduction (-20% to expenses).
Example B: A Beta level core, with a max level of 10, is assigned to a captain a ship in the player's fleet. They function exactly like an organic NPC captain, but can only go up to level 10. The skills that they can learn on level up will be from the same list, too.
Example C: A rare Alpha level core is found with a max level of 20 and the player decides to use it as a colony administrator. Again, this pulls from the same planet governor skill lists as regular NPCs, as well as all the possible specialized buildings as well. The player then puts +2 into heavy industry output, +8 into station cost reduction (-80%), +5 into stability and the last +5 into planet defense bonuses. Of course it will probably take a good 20 years for it to learn all this stuff, so that kind of power comes at a significant cost in time.
When a player removes a core it retains the skills it has learned, to prevent people from exploiting a single AI core to be used across several different types of job. The advantage of AI administrators and officers is that they won't count towards your hiring limit and require no pay.
Meanwhile, only the fuel facility and the heavy industry site have specialized gear. Let's see more types for all the building types to add variety (and avoiding stockpiles of redundant units once your colony limit is reached).
6: Research Labs. Good gawd, hunting for blueprints is tedious. For those who'd rather just throw time and money at the problem, this would make a great alternative. Pick a blueprint that your don't already have, chuck cash into a slider bar and wait. Easy.
7: Repair Facilities. Why do we have to fly around in space with a full crew in order to repair damaged ships? Why not just drop them off in drydock and let your peons do the work for you? Can rapidly heal regular damage (a lot easier to fix a car when it isn't, y'know, being driven at the time) and could also slowly remove major "orange bar" damage as well. Also allows more efficient scrapping of ships, getting much more material out of them than when trying to do the same thing in space.
8: Embassy. Stealing an idea straight from Tropico, this building would have a pull down option for which other faction you wish to target. Every month your relationship with that group goes up by 1 point.
9: Hydroponics. For those who really want to be able to farm anywhere, have this option for all those planets with no viable farmland. Works like a regular farm but costs twice as much in upkeep. Simple.
10: Comstar Stuff. Not enough "stable positions" in your system? This specialized building type combines the nav bouy, sensor boost and communications sat perks into one safe place on the ground where no bad guys can get to it. Of course it's costing you a valuable planet slot to do it, but hey, nothing is free.
