I personally believe Hybrid Special Plots should be a third option for them. This way you can turn on/off hybrids and any further special plots that might come up. They may require their own tab if you come up with enough of them.
The 2x Dyson spawn does not need to be nerfed. It is handlable even if you're late getting to the Dyson. It's not PRETTY, but it's manageable. A defensive overload/fumble can also be recovered from, but it is expensive and you need to be rebuilding the 'lockdown' defenses while your fleet handles the fumble.
If you hit the Advanced Hybrid Superplot, you're screwed. Run. Run very fast or have an inane defense up. Take the extra dyson spawn and build a military post on the planet, preferably MK III, you're going to need the turret boost.
Chasing down Super-Hybrid before it's ready to park and build the antagonizer can be an effort in futility. The bugger is wily as heck and does NOT want to die. It will run. It will hide. It will break for the AI homeworlds. You can annoy it but killing it will require trapping it somehow.
Siege Engine ED:
Please don't touch this. I LIKE this effect. Sure, some of my fleet whines about being banged about a bit. These are mostly defensive fleets and they have Engi Is nearby to deal with it. What I'd like to see is the command station 'extras' be anti-siege. Metal/Crystal Converters, Human habitats, and whatever the other one is called. They can take the FF hits though so its more annoying then problematic. The anti-engine damage though is one of the reasons I've started bringing Siege's along with my main fleet. They're viable now in a fleet ball, and can help keep a line or two of attackers coming in from one direction slowed up while your main fleet deals with another vector.
Sieges don't show up in the AI's hands enough that I think they warrant a nerf based on AI usage.