Ignoring the whole seizure controversy with this episode, this was an interesting episode but not one of my favorites. I liked how it moved away from the normal setting in the natural world and in cyberspace. And I'm sure Nurse Joy installed the virus protection software and wasn't aware the gang were trapped in cyberspace so if she already installed it before hand they wouldn't need to go into cyberspace. And the virus protection was missiles that will emit flashing lights. I think this episode is kind of convoluted in a way but I have a hard time explaining it.
Now I think the main problem with the whole seizure scene is not Porygon or Pikachu. It was the vaccine missiles because they emit strobe lights when they explode. If they used normal explosions instead, this episode would've been safer, but I think they went for the strobe light explosions because it looked more digital.
It's a total shame this episode only aired once anywhere in the world, Porygon's evolutions will probably never show up in the anime, and that the official companies and sources never even acknowledge the episodes existence (Much like Nintendo never acknowledges the Cdi games). I'm just really glad that someone was able to video tape it when it aired because that was the only way it could be on the internet at all. If no one video taped the episode, it would be totally non-existent.