The mapeditor is nice, but it has some problems.
First, you cannot create/import custom ships on the map. Next, I find it kind of hard to use. Mostly with deleting stuff though. Thirdly, the randomizer needs doing. You should be able to set how you want it done. Like how you set up a galaxy regulary; tight clusters, planet numbers, asteroids, minors(maybe), habitable planets, anomolies. Finally, there needs to be a way to customize a planet. Put bonus tiles on it or put improvements on it.
Also, when you build a starbase you should be able to put what improvements are on it. Choosing what techs a race has researched should also be included.