Some replies:
I've never hear of the Thrones game you're talking about, but I based the mechanics on the Axis and Allies board game.
The map is arbitrary, really. Anybody can make a giant picture, throw on some SE4 planet portraits and then draw some lines between them.
The one provided can be considered an example, with harder/easier starts for handicap purposes.
In the game I played, the number of colonies didn't really enter into it anyways. We both got one colony built, and then fought and glassed before any more could be started.
Once we got into the flow of things, there was very little downtime.
While the other guy is pondering his movement, you take a look at your mitt full of components and decide what ships you're going to build.
The administration is mostly "Ok, 10 bucks for my homeworld, 2 for the little colony, and toss back 5 for maintenance. Grab 3 more component cards."
Repairs are rare, and a lot of the rest is special case items. Buying mineral miners on the colonies is a quick given as well.
The hidden orders would take a long time to write down and then unveil properly, I think.
Victory conditions were mostly unspecified.
If you lose all your stuff, you're obviously out, but house rules for victory are easily added.
Research might stand to use more items, but too many tech modifiers to the components could get hairy. Its based on AnA; most of the time you don't have the funds to devote to research instead of bolstering your defenses.
A simple modification might be to collect one coin for each research facility, and put it in a special research pool to spend on a roll when you get enough collected.
The damage is fairly simple.
Components are either flipped over (damaged), or removed permanently (destroyed).
We arranged the ships around the planet/sector they were in, and it fits 4 ships fairly easily (components were partly piled to avoid spillage)
More than four ships starts generating combat penalties, so the fleets shouldn't get much bigger.
We also only used one page of ships, since we were tired of cutting, so we were limited to three of any one type of hull and that helped keep the numbers down too
As for construction, we simplified it a tad, by just laying down the components with the hull, since the surprise is minimal, and events during the turn never conspired to require a different design.