Well, if you dislike anything without a campaign you are gonna run into a hitch or snag or the utter end of all life in the universe before you find anything else on par with Homeworld.
I'd recommend looking into Star Ruler and Flotilla regardless, though.
Well.. I have remembered an RTS, you don't control ships in it, but it's very story driven and has an epic campaign, and it's Sci Fi. If you're interested it called Ground Control, I remember it having two parts, played personally the latter and found it amazing.
--------------------------------------------------------------------------- For Macaragge.
Yeah its fun to start with, but later.... it won't be :P
...y won't it be fun later?
@shotgunmaniac: yea...u're right. barring Homeworld there isn't much out there in terms of space based RTS with a story. as i said before..its a dying genre. still playing SW Empire at War and Forces of Corruption to fill the void.
@ZS: yea...i've played Ground Control 2. its a fun game though not a purely space based RTS.
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You could also look into Distant Worlds and its expansions. It does have a storyline, but not a campaign based one, it comes up as you are exploring the galaxy's ancient ruins.
Otherwise the only other one I can think of is AI War: Fleet Command and its attendant expansions, it only really has much of a story with the Light of the Spire events enabled
[Edited by ZZGashi, 6/24/2012 1:33:47 PM]
[Edited by ZZGashi, 6/24/2012 1:34:16 PM]
--------------------------------------------------------------------------- “Believe those who seek the truth, doubt those who find it; doubt all, but do not doubt yourself.”
Salvation Prophecy is a military space epic. Human, mutant, and robotic factions are at war for galactic domination. Battles rage as space fleets collide, and planet invasions clash against fortified enemy colonies. Yet the greatest danger is the impending annihilation foretold by an apocalyptic prophecy. You must seek out the mysteries of distant alien worlds, and master ancient powers to withstand the coming storm.
Space Combat
Engage in epic space battles with 50 fighter ships, space stations, and battleships. Upgrade your ship with more powerful weapons, missiles, engines, shields, reactors, and EMPs.
Planet Battle
Embark on drop ship missions to invade enemy colonies. Battle against enemy troops, turrets, flier-bombers, and powerful mech units.
Alien Planet Exploration
Navigate your ship through unstable wormholes to unknown galaxies. Explore alien planets inhabited by dangerous creatures. Discover the secrets of an apocalyptic prophecy. Seek out the guardians of ancient runes.
Military Command
Gain ranks by completing missions. Rise up to lead your faction's military strategy. Construct planet colonies, space stations, and military units. Order new missions to attack the enemy.
You should also take a look at Nexus: The Jupiter Incident. It may be more RTT than RTS in that some times you only get control of one ship, but it's very nice looking and fun to play.
I've played a bit of it (stuck on a mission atm) and it has a very interesting campaign/story.
...y won't it be fun later? 
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