I’ve been trying to use the random map creator to make a 3 star map to my tastes, but I’ve run into a problem, every time I enter the settings and create the map, I end up with players starting on a planet with 2 nearby planets, but then there’s a long phase line to the rest of the system. Is there a way to stop this from happening? I don’t want the player’s starting positions separated like this.
I've figured this out, as I too was trying to make an enormous map of epic proportions.
Every 'start' area is a Terran planet with a neighboring asteroid and a volcanic/ice planet. These start areas are completely independent of any map settings - so those short lines are simply like that by default. Now it's important not to make my mistake and in your endeavor to create a huge map you don't make it TOO huge. I let the AI play for a bit because I lost perspective of scale, and when one sent out a scoutship, it'd have taken about five minutes or more to get to the first planet.
I want a 'realistically' sized map, but that's ridiculous

The second thing is that start areas are always on the outskirts - I believe that on the 'min/max' sliders, they're always at the farthest edge - so if all your planets are set in on the close side of things towards the stellar body, your start areas are going to be laughably far away.
A few solutions is to decrease map size (as this will shorten all your phase lanes) and, most importantly, decrease orbit distance.
Personally my problem with the map editor is finding the settings I want - I have a mix of 'mandatory' amounts of planets and a few 'random - x' choices, but I'm just never happy with the result. I'm hoping someone makes a decent ENORMOUS map that's well-tailored to what I'm looking for to save me some asspain.