A think some of the Mega Events could use a boost, as they aren't disruptive enough.
1) Pirate Colony. This one isn't much of a threat and is easy to concur. I think that what this should do is essentially unite the pirates into a major faction where all pirate starbases start to generate influence and can build asteroid mines, perhaps at a reduced price, to give a boost to the pirate colony.
2) Dread Lords. Depending on where they spawn they can be a threat or a minor hindrance. If they spawn far away and they have time to expand they are threat, if not just a free planet to take. I suggest increasing the quality of their planet to 25-30, giving them more bonuses and a unique planetary improvement that gives a boost to all planets in an empire, I am not sure what the boosts should be, but it would also serve as a reward for taking their planet.
New Mega Events:
3) Minors' Alliance. Essentially the minor civilizations all unite in a single major civilization that has its leader and ship style at random from its possible members, as for the tech tree perhaps from the minor that has the most tech researched. I'm not certain how to handle traits and abilities.
4) Something like the Jagged Knife or other alignment events from GC2, where whole colonies defect and form a new major civilization.
5) Wardens Awaken. Arnorian Warden starbases, from the Snathi DLC, appear on the map round precursor planets, artifacts and anomalies. When defeating a Warden starbase research points are awarded based on the tech age.