Lacking QA - I agree.
Pirates - where not a real threat in pre-Crusade, so that I modded them to be stronger
But I agree, not much to be seen from them in Crusade.
Minor Civs - I agree.
Too few events - I agree. But I would also like to see stateful events so that you could set up a variable event chain to be able to tell stories.
Too few idelogy options - I agree, also too linear.
Too few mercenaries - I strongly agree.
Too few citizen names - I agree, but not that serious for me personally.
Everything visible from turn 1 - Principally I agree that there should be more exploration and development possibilities. Whether that should be achieved by a ressource system like Civ 5/6 is debatable though, but is a viable possibility.
Trading - I agree partially. Trading resources seems to be pointless from the second or so unit on since the value decreases dramatically with every unit you add. I often end up trading one unit of every special resource plus one unit of normal resources the AI doesn't have what is a lot to click every time ...
Invasions - I agree, the system falls very short of what was promised. I somewhere made some suggestions before Crusade how an invasion system could work, but can find it right now and have no time to make new suggestions just now 
Turn time - I also see a decrease from a certain point on, but I tend to play very slowly and don't mind reading while waiting for a turn to finish, but that's just me 
Difficulty - On that I cannot comment that well since I only play very slow games on gifted and didn't end a single Crusade game yet.
Tall vs. wide - I have the impression that colony rush is still a widely adopted behaviour by the AIs, but I also found some which didn't spread so far. Whether that is because they have another tactic or only because they didn't find suitable planets I cannot say.
Brad factor - I like Brad's intervention and trust that he has a good relationship with his employees
Although some of his decisions seem a little bit rushed 
Little whines - I have those and some more ...
Map selection - Since I don't see the map layout because of FOW I don't know at the start whether everything is good or not, but that is just as well since that's one more challenge 