Yeah I'm still working on my mid-game myself, especially since every race plays mid-game differently. After you have the big 3 techs(Applied Casimir Effect, Non-Baryonic Particles, Infinite Supermarkets) things open up a lot.
My next goals tend to be military for unlocking lasers and fighting pirates, Colonial Rights to continue expanding and the Moon Exploration tech to fix some of those pesky planet penalties. Beyond those its pretty open and I just go with my gut for what the game needs.
As far as colonizing/expanding you really have 2 options: if you aren't getting hemmed in by other races you can keep throwing colony ships so long as you can manage Happiness/Dust OR you can build 3-4 fleets of destroyers and take those systems from someone else but much more slowly due to the newly captured colony penalties.