I really enjoyed the hours I played this a few years ago, where drone attacks were first introduced, but since they were pretty limited I put it down for a while. How has the PvE missions/goals/defense stuff been changed? Is it more robust? Thanks!
Base game - lots of stuff added, but fundamentally, not really. Base attack can still be pretty much ignored with a few turrets up. I would suggest the mod eden reforged, but if you are not a fan of CPU you will probably really really hate the crippling CPU changes in this, so maybe switch that off as the rest of the mod is a huge improvement over the base game.
Reforged Eden is a custom scenario (Project Eden) made by a player, merged with an extensive customisation of many game aspects (Reforged Galaxy) made by another player. You can get it from the Steam workshop. If you want to see the state of Empyrion (the default game's missions) then stick to the default game, many missions have been added and are still being worked on.