I don't think any of the 3D Sonics have been related to any of the 2D ones. The plot pretty much stopped after Sonic and Knuckles. I know Knuckles backstory remained the same, but still.
Sonic 2, 3, and Knuckles all happened right in a row with no time gap in between, I was always a little curious why they never just continued it from there.
Since they're going back to making this 2D, I do wish they'd just make Sonic's legs just turn in a circle again, he never looks like he's going as fast without that.