I think the very first frame of the video is a real factor. The DX port was unfortunately the introduction for most players (and probably after being exposed to SA2 Battle first). For a long time if you didn't have access to a Dreamcast it was hard to know how much better the original is even if you'd heard that it is. There were always screenshots of the different character models but the rest of it wasn't as well documented.
The Dreamcastify blog is the most thorough documentation of the differences I've ever seen. It puts wikis to shame.
Otherwise, trends are a thing and timing is a thing. People are going to go with the flow and dunk on the bad game. There's always going to be a trendy pushback, but it took a long time for that to build. The game's flaws are obvious enough that people didn't know how to say it's not that bad. It kinda is that bad. The good parts were still there, but they were lost in a sea of wholly fair criticisms.
I think the Game Grumps playthrough was a turning point. It had its moments. My first Big playthrough took four hours, so it was very cathartic to know I'm not the only idiot. The problem is Arin wanted another Sonic 06, and it's just not, and the transparent attempt to make it look worse than it is gave grounding for the pushback to finally get going. It's not
that bad. I don't know if this was directly related to the Dreamcast version geting more attention or just some lucky overlapping timing, but I think it all goes together. The game deserves better.