How Megaman X6's Plot Should Have Been Written IMO
I always thought Isoc being a Dr. Wily reference should have been the main villain, not Gate. Isoc doesn't need to be Dr. Wily, maybe he can just be a robot who has Dr. Wily's brainwaves which makes him think he is Wily. I would make Gate and Hi-Max the lesser antagonists working under Isoc. The plan would be to further link Megaman X6 to Megaman X5. That would mean that Hi-Max would be the first fortress boss, second is Gate and the third boss before Sigma is Isoc. This of course, I would try to create some hints that Isoc is Wily before dismissing it.
Isoc's scheme would involve Zero and the Nightmare Virus to taking over the world. With Sigma supposedly out of the way, Isoc will try to take over. He revives Zero as an evil menace which can only be recovered after Megaman X defeats him. However recovering Zero will not stop him since he has other plans. He decides to send Hi-Max and Gate after Megaman X. He would sound like he had a grudge against Dr. Light, try to make him feel like he is Dr. Wily.
So how will I deal with him as a boss? He gets Zero's DNA and reveals his latest machine. I would create it like a Wily Machine which is powered by Zero's DNA. It will just be a one round battle. Once its defeated, two outcomes will pop out depending on whether or not it is X or Zero. Isoc then begs for mercy, tries to double-cross them by reviving Sigma which only leads to his death.