Seeing how SE got it's start from the pen and paper game Starfire (which is actually going digital from what I hear - though as a "quasi real time"), how about Starfire "jump engines"...
Still use warp points, but you can jump in system by 1 or 2 squares... Would make minefields actual fields, and Warp Point defense would suddenly become more interesting.
I agree with the borderless combat map, and I could go either way on the interface (though standard windows is easier to hide at work

)
Another idea: Space Yards with multiple docks/slips/whatever. You can build multiple ships at once, but the space yard resources are divided among them. So you wouldn't have to scrap that half done Battlecruiser if you needed another escort or transport in a hurry.