Pirates? turn off barbs in options
AI too stupid? change to the harder difficulty levels, prince (AI still not to smart) or monarch (AI gets a little smarter). Moving to the higher difficulty level in this mod is NOT like the civ games, it doesn't effect how long it takes to tech something, build something, etc - but only makes the AI smarter.
Scouts? on auto, they do bring you some results with finding goodie-huts/wreckages, but as soon as you've explored the area immediately around your first planet build for additional planets to expand on, just put them on auto and change to building Stealth Ships (comparatively, the change from scout to explorer in Civ). Additionally, as a prelude to attacking an AI, having several stealth ships INSIDE their borders destroying warplanes(roads) and killing construction ships is KEY to beating the AI on the higher difficulty levels.
Colony Hubs? Starbases do exactly that by using a construction ship; put them BETWEEN your established planets next to resources
Unhappiness and sickness? Discover the advocates (survival, wealth, knowledge, power, religion) and help get rid of that. As well, each of the "civs" seem to do better under different civics
(note that some of the civics which are GOOD in Civ, may not necessarily be good/do the same thing in Final Frontier)
BEST GUIDE and game/mod walk-through?
http://gaming.download-warehouse.org/civ/