I can see how Sonic 4 is tricky at the get go, especially with our muscles remembering how to play a classic game, though I can't say that Sonic 4 is a difficult game from start to finish. More like it's different for the first act and then you get it around the end of Splash Hill.
To bring up JSR vs. JSRF again, I remember how bizarre it felt to play JSRF after playing JSR a dozen times through. After a while, JSRF became second nature and I hardly noticed the difference.
Or Chaotix. That game felt so odd when I first played it last year, but after a bit I was running through it as naturally as Sonic 2. Sonic CD, however, I still have yet to get used to that game's spin dash.