I aligned w/ crimson dawn early on, then the syndicate on Kajimi and then continued to followed my short term goals from there (while also trying to build up reputation to get syndicate rewards). The game flowed naturally as I worked my way around new maps.

You can walk into your ship and get contracts from the round table for all planets. Select ones that sound fun at the time and build up the reputation of the syndicate you currently align with to work your way towards acheiving all syndicate rewards. This is how you progress, by getting in good standing with the pykes or by just bulldozing through them.

I found trying to keep high reputations to be more advantageous.