I've found through my plays of Eclipse that there are 4 things you can do to speed up setup:
1) Take the bags where you put the ships in for each player. Add 3 colony ships, the storage markers, the starbases, all cubes and disks. You'll have a bag for each player with all the stuff they need to setup their player board.
2) Buy a 'bead storage box'. Craft section of Michaels or Walmart. Put your sorted upgrades in here. Setting up the supply board is as simple as taking the lid off of this box and placing technology tiles.
3) Buy some Population Trays off the internet. These are specifically for eclipse. You can buy the ones with lids and that will let you store all the cubes for a given player in the tray. Setting up a player board is as simple as opening the lid and dumping the contents of their bag next to the board.
4) Have all other components pre-sorted and bagged seperately.
It takes < 5 minutes to go from putting the box on the table to making my first action with this setup.
Population Trays: http://www.beklaser.com/en/6-eclipse