Sins has more atmosphere. Planets in Sword of the Stars always looked generic and rarely had any clutter other than similar looking asteroids. In Sins each planet is covered with orbital platforms.
Sword of the Stars has no fighters/carriers and the dev team will tell you to go to hell if you ask them for fightercraft.
Sword of the Stars ships look cartoony in comparison. Don't believe the guy above me, he must be playing Sins on crap mode.
Sins rarely gets to be an organizational nightmare because everything is at the stellar level instead of the interstellar.
Ironclad was definitely the better part of the Barking Dog team, I'm sorry to say. And I'm a guy who loved Sword of the Stars. It just can't compare with the polish on Sins.
Also Tom Chick hated Sword of the Stars and loved Sins of a Solar Empire, so I guess that's a difference.
Moving defence turrets. They are not stationary and allow a global coverage of your system.
If by "global" you mean "orbiting very close to your planet while the fighting is going on on the other side of the map. Global my ass. Also, the whole moving around thing was implemented poorly and makes it a game of Star Wars bumper cars. Yeesh, how could anybody compare it favorably?