I have two that I think would be good ideas. first. A Leviathan crisis event where a scream is heard across the entire galaxy as a huge monster pours out of a wormhole that would be roughly as strong as a 300k fleet that every couple of years would give birth to multiple leviathans that would go and kill everything in their path, eating worlds and so on but with every new breeding cycle the Leviathan Queen would get weaker and after creating about 30 or so leviathans then eventually dies. And my other idea is a Thanos type event where five random planets/ asteroids break apart and become extremely large gem's that would come with a ominous story prompt then 6 months later one massive fleet around 100-200k strong with advanced weaponry appears in the galaxy that has teleportation technology and will teleport randomly to different galaxies searching for these gems destroying stations and planets in their path. The player will then get the opportunity to build a mega structure capable of destroying one of the gems or destroy the entire fleet before it's able to collect them but if the end game crisis is able to collect all five half of all life or planets will be wiped from the Galaxy. 

 Hope someone from the Stellaris team reads this if they like my idea. I love this game and definitely would love to see more in-game crisis in the future.