The first thing they should get rid: The restriction of a single Crisis per game.
This restriction goes against the core ideia of Dangerous Technologies. After any Crisis happen, you can rush and get all the Jump Drives and Synths you want. They should just make that every time a Crisis start, you multiply the Mean Time to Happen of the other Crisis by 5 or 10. So, MAYBE you can have multiple crisis Happening at once or nothing at all. Or other Crisis will just appear at some time after the first.
Second thing: Get rid of the "true random fuck you, you can't control what you are doing" of the Crisis, because, in fact, it does not matter, a Crisis will spawn anyway, so you simple research jump drives and synths, who cares? You can't do nothing anyway.
When you Research and use the Dangerous Techs, if you abuse it (too many ships with Jump Drive and too many oppresed Synths), things will start to get weird and you will get Notifications from your Scientists that you should stop abusing the Tech. If you don't stop, things will get worse, like Unrest in planets with Synths will increase dramatically, have strikes and shit and your Ships will randomilly be Missing in Action. If you STILL don't stop, there will be terrorism by Synth blowing Buildings and killing Pops and a random Unbidden Armada will apear from a Rift and start to attack your planets.
Finally, the Unbidden Portal will appear inside your Empire and start to fuck you or the AI World will spawn close to your empire and sabotage and rebel you to hell.
This way you can control the consequence of the Techs and make the Crisis not a inevitable thing that you don't care after the first one.
When other Empires start to mess with Dangerous Techs, you will get a Situation Log about how shit is the problem in that Empire (Level 1 [notification] to level 5 [Crisis]). So you can make a War to stop the Crisis from happening, Banning Synths and Banning Jump Tech.