Without question my favorite RTS would have to be Pax Imperia: Eminent Domain. It's a space 4x made in 1997, and as much as I do like Sins of a Solar Empire, Pax Imperia walks all over it in a number of places. If they could just merge SOASE and Pax2 to make SOASE 2, it'd be almost perfect.
In Pax2 the strategy starts before you even start a game. You have something like 8 pre-made species like virtually all space RTS game...and you skip right past them and design your own species! It's a basic point system where you control about 30 different things. Temperature tolerances, atmosphere, various traits like warrior, trader, etc. How fast you are at different researches.
Next is relatively standard: set parameters for a randomly generated galaxy. You have to use wormholes between pre-defined systems, so you can actually set up blockades and defend your core territories, etc. I actually prefer this to free roam systems.
Then comes the research. 5 categories, each one with 50+ research to perform. Nothing too spectacular by itself: but the ship research does not automatically apply to your ships. No: You have to actually design the ships yourself. What shields, weapons, fighters, etc. You can save designs allowing you to have different styles. For example, a mine-clearing battleship. You must then have your current ships upgraded.
The biggest con for the game shows up then though: The combat system is pretty poor. You have fairly minimal control, most of the time you just hit the auto button and wait to see what happens. Also, any time you are in combat, everything else pauses.
Planets have nice defenses though, another all too often missing feature. Minefields, battlestation, missile station and a fighter station. All can be upgraded 5 levels and the minefield can be smart tracking mines with some research.
I still play PAX2 to this day. Yes, it's relatively easy to get this game made for windows 95 to run on windows 7! I have games for XP that give me just as much trouble. Granted, I've yet to get multiplayer working on my windows 7 computer, but a friend did without doing anything. <shrug>
Oh, I also have to make a shout-out to Imperium Galactica 2: Alliances. Want to take over a planet? You've gotta land tanks on the surface and destroy their defenses. With the surface of planets able to be designed by hand, this can be a bit of a challenge and a fun addition. Adding this to the above Pax2+SOASE would quite possibly be the perfect Space 4x IMO.