Firstly I want to say that I have Epilepsy, and I experience Grand Mahl seizures as depicted in this flash.
I thought how you began your story was very funny, at first when he had the first seizure i was like thats not cool, but then they started to party and i literally laughed out loud. The Mission briefing I thought could have been better, I will have seizures and tunnel vision right before them and try to brace myself sometimes, and coming out of them I will be groggy and semi-coherent with a massive headache and usually bitten my tounge which can cause speech imparement and bleeding, i think in the mission briefing as well as at other times throught the flash he could have been semi-coherent but unable to really speak, you could have turned that into a joke, like "Do you have any questions? I take it from your silence your senses must be perfectly balanced heading into the mission." The foaming at the mouth was a little much for me personally but i can see where some might find that funny.
The evil villian thing i think could have been done better, I thought he was gonna have a siezure and knock him off the balcony, that would have been cool. The self destruct button was an easy way out, you could have had him fall off the balcony and land on a generatior that powered the doomsday device (whatever it was called) or had your epilepsy hero smash his face into the control panel and overload it or what i think would have been good would be to let him drool and bleed all over it and short circuit it or even cause it to like shoot some astroid that was also nearing earths orbit and make him earn some kind of medal.
I didn't have any issue with the animation because I see a lot of it like this, but there is obviously room for improvement. And I agree with what others have said about the audio in which there were points in which it was choppy like with the villian. However all of this said, I think there were some really good comedic elements displayed and this would have probably made an even greater flash had you focused on those elements rather than the action direction you went with.