There's a cuople of files you need to tweak:
Firstly, in galciv3\data\game, you need to change mapsizedefs.xml:
In there, you'll find 'base'. Base is the seed number; more or less everything is determined by multiplying or dividing this number - higher means more stars, more planets, more habitables.
You'll also need to find 'maxhabitableplanets' in the same file. This is a hard limit on the number of habitable worlds that can be generated on a given map size. You can set this number to pretty much anything; I've put it to 999999 so that the setting has no effect.
Then find galciv3\data\game\starsystemdefsf.xml.
In here, all the various possible star system configurations are determined. Look for 'habitablezone' settings (there's one in every system template). This is a hard limit on the range of habitable planets that can exist in a given system type. Adding 1 or 2 to the minimum and maximum scores here will generate more habitable planets.