Mashiro hit it on the nose with Sonic and Knuckles. S&K would be considered Sonic 3.5
Playing with Knuckles or Tails makes the difference. With Sonic, he got to use the shields to their full extent. He'd get a fire dash with the flame shield, the double jump with the electric shield, and the bouncing effect with the water shield. The other two can't do that, only use its passive abilities.
Tails could fly and swim to areas that Sonic alone couldn't go. Even then, Tails couldn't carry Sonic in the water. Knuckles couldn't jump as high, making a few bosses a little tricky. Also, his gliding abilities gave him some extra offense since his knuckles could pierce some enemies, making him a real airborne threat in comparison to Tails, who had to watch where he was going. Climbing up walls made for some interesting strategies (especially when locked on to Sonic 2), try it some time!
I haven't completed MP3 yet, but what I can say is that with this title, Retro has completed in assimilating this franchise as their own. They did things that Yunpei and the old R&D 1 wouldn't even consider. The single act of making Samus a part of an overall conflict, interacting with non-hostile people is a 'Prime' example (no pun intended.)
The last segment is definitely one of the best this year. I'll save my other comments for the other thread.