I don't think it's Farfetch'd (HAH!) to say he could take out most of the people in the Kanto region. It'd be really difficult to get them all, and if one of them has a Pokemon on hand he probably couldn't do it. Almost any Pokemon has something he couldn't beat, but he could manage to do a lot with stealth and gear.
But if he comes across something like Golem, Rhydon, Dragonite he's totally screwed without surprise.
Are you limiting the region to just the first 151 Pokemon?
Killing Pallet Town will be easy, only trainers there are Blue, Red and Professor Oak who, at this time, should be sleeping. Route 01, no problem either. Snake is a good tactician, he wouldn't merely attack Viridian City, someone would escape and make his attack publically known, giving Kanto a chance to counter react (he could wait for night until attacking Viridian, but then, they would find out about the murders in Pallet). Snake would, with time, be able to take over Kanto, IMO.