Crazy Awesome: Any awesomeness in the setting will likely be crazy by default. That goes for events as well as characters.
Critical Research Failure: These sorts of theories are the principles on which Wonders supposedly operate. Many Geniuses realize this is not how things actually work. Fortunately, belief in their explanatory theory isn't as important as the fact that they supply an explanatory theory and build their devices accordingly.
Genius Bonus: Appropriately enough, there are plenty of references to be enjoyed by science and history buffs alike.
Jerkass Woobie: A number of antagonists. Lemuria is full of Geniuses who were simply snapped up before they learned what Mania really is, and former Peers who just couldn't live with knowing they're crazy anymore.
Special mention goes to Seattle's Argentine St. Croix, who, extramarital affair and killing her Stalker with a Crush aside, lived a relatively blameless life prior to her Breakthrough, and never wanted anything to do with Inspiration in the first place. Oh, and one of her sons is in a coma that even mad science can't fix. The other one publicly disowned her in a fashion cruel enough to shock some of his new allies.
Even Clockstoppers are sort of pitiable. It's not their fault they're spite-fueled avatars of ignorance. Probably.
Not to mention that, being a bit odd, Staunens can get like this:
"So I spend a lot of time staring at the sky, and not looking at your face and thinking about squirrels."
Scrappy Mechanic: The constant drum-beating on how expensive mad science is makes reading the book kind of a chore. Imagine playing with a Storyteller who insists on holding to that.
The Woobie: Three out of five Catalysts (Grimm, Neid, Klagen) are likely to involve a personal tragedy. In addition, all Catalyzations are generally traumatic; a person who becomes a Genius is a person who has been driven insane. It's probable that there are many, many Inspired Woobies.
Katastrofi: Doomsday devices; the rulebook's sample 5-dot weapon is a cannon that can demolish whole city blocks at a time, described as "some silly thing a Genius might make while trying to take over the world again".
Metaptropi: Permanent invisibility to the 5 mundane senses and magical detection for only 6 bound mania.
But the fact that Prostasia can provide insulation against Havoc at any level makes it endlessly useful. Gotta love form-fitting force fields.
It's also worth noting that maxed out Genius armor gives a default Defense of 7, compared to a mundane bulletproof vest's Defense of 2. And it can go higher.
Prostasia as of its improved rules: Nigh-invincible fortresses. You say your orbital doom cannon just delivered 50 successes' worth of damage to my lair? Awesome! You'll need 150 more in that single attack to scratch my paint job.
There is also the Apokalypsi 2 universal translator which gives translator microbes to everyone is range. You can make a universal translator the size of a CPU tower that has a range large enough to cover the earth. While it doesn't give you godmode it would make a HUGE impact on the setting and completely mess with the masquerade. A starting character can build this.
If you combine Assembly Line 5 with any of the above, well... God Mode
A theoretical Game Breaker within the setting itself is the Axiom Pankosmoi, AKA Apekrina, AKA the Needle Grail. If it's real, this Axiom could prevent Havoc, enhance Inspiration, and even generate/harvest Mania from reality itself... somehow. There is no evidence that Pankosmoi actually exists, but mastering it would be tantamount to achieving godhood.