from Deviantart:
Ok, this comic has a pretty interesting backstory. It all started when I was doing the whole Snake communicator thing on the shadow moses island stage in Brawl. Thats where you gently push the down taunt for a split second and Snake talks to his comrades from Metal Gear for a little while. Well, when I got up to Sonic, I was surprised to hear Snake say that HE DOESN'T LIKE HIM! I was like "wtf?! Snake doesn't like Sonic?" Snake didn't tell Otakon WHY he didn't like him, so I did some research. I started with rumors, one was that Snake saw Sonic as competition for most popular 3rd party member, another was that in the wild, hedgehogs eat snakes, but the third rumor was most convincing...

In the original Japanese, Snake's voice actor is Akio Otsuka, who is the son of Chikao Otsuka. Chikao Otsuka is the japanese voice actor for Dr. Eggman. That is why Snake doesn't like Sonic! Its because he's the illegitimate son of Dr. Eggman!!! I lawled, and had to do the whole Star Wars joke thing because I'm a nerd.