Sword of the stars. The battles are in real time.

Better than sins?  Do tell.  Why do you like it so much/what is excellent about it?  Thanks!

First of all, I should say that I usually prefer TBS rather than RTS and even though Distant Worlds is a RTS, it is pausable at any time so to me it plays much like a TBS game. So basically it isn't a click-fest. People who prefer games like Supremacy or other click-fest games are going to get bored with Distant Worlds.

As far as the game itself is concerned it is seriously unbalanced. If you scout enough there is a strong chance you'll find a game-altering starship or ship grave-yard. There are also some unique planets in the game (you can play with hundreds or thousands of systems consisting of multiple planets) that will boost certain aspects of your production through the roof. Its funny, but this 'unbalance' makes the game really fun because it can flip on its head at any time. If a 'friend' finds one of the unique planets you need to really think hard about letting them develop it or to declare war and take it yourself.

Running under the strategy game itself is a whole trade and civil system that you don't control. The AI controls this for you. You can build military ships and support ships but you don't decide on freighters or trade. If you take planets outside the range of your civil freighter range then you won't get the benefit of certain resources until you build a star-base network to link everything up. This aspect works really well once you know what is going on because you need to develop the network but have no control over how it is used by the freighters.

All aspects within the game can be automated to varying degrees. If you don't like colonising or planning and only want to control a single fleet (or even just a single ship) you can do so. If you want to micro-manage all aspects then you can also do this as well. When I play I have most things on auto but I usually over-ride certain aspects once I see unique opportunities. I usually also control the attack fleets but leave the system defences on auto. With potentially hundreds of systems to manage it could be a nightmare without this automation.

There are many different races in the game that each play with a nice unique flavour. Some are militaristic, others scientific, etc.

Here is the main page at Matrix.

The games that I've tried so far in this or a similar genre:

SOTS
SINS
GC2+
X-3:TC
Armada 2526
MOO1,2,3
Planetarion (browser game)
Star Ruler

The ones I have not tried that I've heard various interesting things about is:
Star Empires IV, V
Distant Worlds

Now, for the first list, I'll bulk them according to features.

Explore
How fun is the game world? Is a planet 'one,normal' or 'a teeming green world orbited by a precursor defence system'. Can you get surprises?
Staple games of ths are GC2, MOO's, SOTS. However, X-3:TC should be mentioned here. As it is a flight sim-rpg kind of game (with the option to build a space emprie) it does this bit really well.

Expand
Colonization. Explore is about how much life there is in the galaxy. How much life is there in your empire? Interesting races? Unique features? Racial traits? Advisors? Research and technology?
GC2, SOTS are good at this. SINS with all the expansions are decent as well. MOO series was good at this too.

Exploit
Diplomacy and strategy. Is diplomacy limited to 'shoot first, talk to the hand' or can you have genuine allies and enemies? Strategic advantages? That sort of thing.
SOTS does the strategy well, with the radical travel differences between the races. Diplomacy is less good, though. SINS, GC2 are good at diplomacy. But here is the reason I mentioned Planetarion - it's massive MO, with hundreds or thousands of players, resulting in coalition building and diplomacy more complex than in any 'normal' game - same with EVE online, incidentally, but it has no empire building so it can't really be counted - but once you're in a corp, it qualifies well enough. This is also where X-3:TC falls through.

Exterminate:
Or, 'combat! What's it about and is it fun?. For my part, I like combat to include ship design and tactical combat, with an option to autoresolve inconsequential battles. SOTS, IMO, is the best of the listed in that, with MOO2, X-3:TC good contenders. GC2+, planetarion would probably be the worst. Stack fights is in my opinion the worst possible option. SINS, while the combat system is good and exciting, lacks the unqiue components 4X games should include, IMO.

Special mention: Armada 2526 and Star Ruler. They were heavily recommended indy games, but for me, they failed to deliver enjoyment. Star Ruler remains a tech demo, Armada 2526 suffers from crashes and lack of being fun (tm).

Another special mention:
Pirates of the Burning Seas. Yes, it's a pirate MMO. It does, however, feature ship combat, exploration, building up a trade empire (if that strikes your fancy), etc. Worth a look now that it (soon) enters Free to Play. And the ship combat? It's brilliant. Probably the best ship combat I've run into, period.

X3 fits right in because you can play it on the "fleet" level - but it's no 4X game at all.
There are no winning conditions.

You set your own winning conditions and do whatever you like. It's a sandbox game at heart.

Large scope battles or large empires will be next to impossible to control without custom mods and scripts... which do exist.
And if the factories, ships, or fleets don't do exactly what you want - you can write your own scripts which control their entire behaviour.

To be honest, there is no RTS game like Sins currently on the market.  It is a thoroughly unique in it's approach and, hence, why it is an established classic of the genre.  This is why you're not going to find anything similar. 

There are other good sci-fi games, though, most of which have been mentioned above.  My summary:

1) Galactic Civilizations II:  Not RTS, but turn-based.  Nonetheless, it is probably me second favorite sci-fi 4X game of all time.  Part of the reason is that is plays sort of like a board game, which is something of a plus in my book.  It has that good "simple to play but hard to master" mix that many other games bungle. It also has the best planetary development component of any game. I definitely recommend you give it a try as long as the lack of a RTS component does not bother you.

2) Sword of the Stars:  My third most-played sci-fi game (my review here).  This is basically Total War in space.  Of all the games, it has the best tech tree around.  However, I find the planetary development to be much too simplistic, and the battles, while a lot of fun, can be repetitious after a while.  Nonetheless, this is a solid entry into the 4X genre with a wide fan base.  I personally can't wait for SotS II next year!

3) Distant Worlds:  This is the latest entry to the world of 4X gaming (my review here).  While the others keep it simple, DW is much more complex.  Nonetheless, I have found it a thoroughly immersive experience with an wonderfully innovative "private market" system that really brings the game to life.  However, because there is a major expansion in the works that is going to be changing some of the core mechanics (a new tech tree system, carriers, and more!) I would wait to pick this up.  The expansion is supposed to be out before Christmas (details will be released this week), so waiting a few weeks won't be that hard.  Also, DW, while RTS, is not a Sins type of RTS.  It is much slower.

4) AI War: Fleet Command:  This is a great indie game and, in many ways, is a lot like Sins in its gameplay (my review here).  However, AI War uses a 16-bit graphics system, so don't expect to be wowed in that department.  Despite that, AI War is a masterful combination of the 4X and tower defense genres where the player has to build massive fleets and carefully pick which planets to take from the AI, all the while defending his own systems with a series of minefields and turrets.  It is a very challenging game and well worth your time.

The only game I haven't tried yet is the campaign expansion for Gratuitous Space Battles.  It's still in beta, so I am waiting.  But I found the core GSB game to be a lot of fun, so this might be good too when it is finished.  Sounds a bit rudimentary, though, so I don't expect a deep experience like GalCiv or the others.

Truth be told, each one of the above games offers something unique.  Unfortunately, none of them does everything well.  I really wish somebody would combine the best elements of my top four games into one super game.  Eh, maybe that will be GalCiv III.     If anyone can do it, SD can!

Thanks!  I really like my sci-fi gaming.

I forgot about that game.  I did try it when it came out (I even interviewed the dev) but it didn't impress me.  However, I've been hearing people say that the improvements made over the last few months really have changed the game.  I've got to take another look at it. 

Thanks!

I'm not trying to discredit your point, but you know you can do this in Sins too right? It might still seem like a clickfest though.

AI War is definitely a nice little gem. The structure of the game is a bit different, though. In all these other games, you and your AI opponents start off on the same foot and build up with you trying to out-do the AI. In AI War, you start with one planet, and the AI has everything else already settled. Your goal is to defeat the AI smartly - just about everything you do that hurts the AI increases its aggressiveness (think of it like the Borg, while you don't mess with them they just go about their normal routines since you're kind of insignificant, but once you start pissing them off you start to regret it). This leads to all sorts of unpleasantries, such that the game becomes very difficult to win (if not impossible) unless you make smart choices on what planets to take.

It is a complex game, there are tons of ships, starships (think Capital ships in Sins, minus the abilities). Some ships can be customized. Some special ship factories might be randomly seeded into the galaxy, so the AI planets with those on them might be high priority targets. There are tons and tons of AI types that (unlike Sins) do actually dictate the AI behaviors pretty well. One might be a heavy Turtler who'll barely attack you but have very tough defenses to crack, another might be an Assassin type with lots of Cloak usage, etc.

The game recently received a graphics overhaul and was ported to a new and flashier engine. It's still the same style, but the UI, particles, etc all look considerably better. The demo for the game has also been updated so you can try it out on the current game version. 

I'd highly recommend the game

Yeah, I'm looking forward to Light of the Spire. Zenith Remnant was a pretty tremendous change to the game (very happy about the Golem buffs in 4.0), and the premise for Light of the Spire sounds pretty awesome. Since those Spire starships are damned annoying to kill (and are quite powerful), I can only imagine the rest..

I stopped trying to keep track of the changes after 4.0, though. Every time I start it up there's at least 1 beta patch, if not more. The 4.0 changelog itself would probably win Guiness World Record for the longest change log ever.

Haegemonia (Hegemony) - wonderful space game similar to sins in some respect.

Try Homeworld and Homeworld Cataclysm. I am surprised no one mentioned them - Haegemonia is a poor spinoff of those games. Original Homeworld is epic in every way, but have flawed gameplay, but Cataclysm is truly excellent.

I've been playing around with Distant Worlds a bit and really enjoying it, but it isn't for everybody -- it is part part RTS, part 4X, part economic sim.  Wish it was multiplayer.

I'm really excited about SOTS 2 next year.

I have managed to restrain myself from getting SC2....don't want to spend $60 just to get bored of it.