Not having any idea what to do is not very related to the expansions you use. I mean, they do add to confusion, but they are probably not the reason.
The only expansion that really changes the way the game plays is The Light of Spire, and you can just ignore the spire storyline anyway.
If you dont know what to do, there is an "objectives" tab in the "stats" manu, you can see some suggestions there. Or you can just go kill the AI. Oh, you cant kill the AI homes because of the shield generators? Then go kill those, grabbing whatever systems you can along the way. Get stuck on some fortified system? Try warheads, or maybe spirecraft or golems, if you have those enabled. Or go hack something. Or stock on mercenaries and then attack with these.