One of my favorite mechanics in SoaSE 1 was that ability to have new ships that are built automatically "waypoint" to a ship or group. This saved SO much tedium and let us concentrate on strategies and watch the action take place. It's the main reason a friend, who dislikes RTS games, plays Sins.
Consider, for SoaSE 2, another leap forward: "Fleet Blueprints". One of my least favorite parts of Sins has always been after battles. You have to play Where's Waldo on a Spreadsheet, trying to see what ships got destroyed; try your best to remember it all; and rebuild it from memory at a planet. A total, tedious pain, and half the time I remembered incorrectly and have to "re-oder" more of different ships.
Let's say for a simplified example, I have a fleet with 10 of every ship I can build in it. I click on "Fleet Blueprint", and after that, any time any ship in that fleet is destroyed, the closest ship factory starts making it, and sends it to that fleet to "refill" it, so there are 10 of each ship again. That would save SO much time and annoying busy work. And it would be a great blurb to put on adds for this version of the game.