hmmm, not quite sure why its doingthat, but heres something that you can try;

go to your stardock/TotalGaming/galciv2/Data/English folder and find the "Custom Planets.xml". FIRST, make a backup of this file and save/copy it to another file (backing up stuff =always good). Then, open it with note pad, (or whatever youer default word pad is)check to see if your custom planets are there;

A) if they are, simply change the size (ex: 0.60 ), planet Quality (ex: 0 ) or whatever else you want to change
if not, put them in there! (you can tell what kind of code you need for each planet and starsytem byt the existing code for the other planets; in fact, might be easier to copy and paste, then change stuff to your hearys desire... whatevers easier) then change the size, quality, etc.

make sure to save changes then double check the altered xml to see if changes were made. then, of course, field test it

-Grae

i don't have any of those options and i have 1.11

So the question remains, is there another map editor, or is there something about gc2 builder I can change, so it no longer creates size 12stars with size 100 planets?

First, do you have the lastest version? Only the lastest has the options.
But, if you have the lastest, you can determine the star size by opening a new map and on the window it opens, click the 'star" button. You can adust the min and max size from there, and the builder uses that info when you create systems. For the planets, you can determine the size by pressing the planet button.
My only complant is that after you change the PQ, you cant tell what planet has what PQ

http://www.gc2builder.com/

Is it possible to get GC2Builder to work with saved games, or only with scenarios?

I used the Custom Planets method to give myself a great home system (note: it ONLY affects home systems), and after a few restarts, managed to get an Earth with one each of +300% Manufacturing and +300% Research tiles. I was developing slowly, and by the time I had ships out to get the other four planets in my system (all great planets), a neighboring empire had grabbed two of them.

The Custom Planets method doesn't seem to give more land area. Mars, for instance, is never going to give you many tiles, even if you set the hab rating to 20 or more. I guess you can change the planetary map being used. (Wish there was a way to set tile bonuses, but it appears random. )