I do not think he is evil, simply out of touch in that ivory tower of his and a terrible ruler in general. Apart from the Strip, New Vegas is a shithole, yet his priority is developping space flight? He has been here for 200 years, yet the very best he could do is muster some weak ass robots and three campy casinos? And if the explanation for that is a bug in his system, well that's yet another bag of worms, is it? How can we be sure a similar bug doesn't happen again? The man is completely dependant on his network working at peak condition to continue; in the event of a technical failure (true, happens much less in the Fallout-verse than in our own, but still possible), the ''great visionary'' can't do anything, or worse is reduced to a corpse waiting for the germs to kick in.
Handling so much power to someone so fragile and so determined to leave everybody but himself and his ego in the dirt is simply not an option. I dislike the Legion and yet I would let them take power before House, hell House is the only faction I never supported in any playthrough.