I think the Sonic hate from the media actually comes from Sonic fans not shutting up about it. Much like the Final Fantasy VII uber fans, rabid Sonic fans come out of the woodwork constantly. From what I've seen (and experienced firsthand in retail), the really hardcore Sonic fans are obsessive to a level that few games reach, and it can be off-putting.
For the record, I never cared for the Sonic series, but I was a dyed in the wool Nintendo fan. I thought Sonic 2 was good back then, but I don't think those games hold up well over time, especially when compared to the Mario games of the same era. But to your point of revisionist history, I get annoyed with that, also. I have remarked many times on Nerds Without Pants that "Nintendo Hard" isn't some badge of honor; it stemmed from people not play testing their games. Similarly, I laugh at how Final Fantasy IX has become a darling of the Final Fantasy series, when at the time of its release the masses hated it with a firey passion.