Sonic 3 alone had 6 zones, you could play as Sonic or Tails, and while Tails had access to some high places that Sonic couldn't reach, they basically followed the same path.
Sonic & Knuckles alone had 8 zones, although only the first four were proper complete stages with two acts each. The rest of them were more like a long and epic final (lots of boss battles and such). You could play as Sonic or Knuckles, and this time they not only had quite differente abilities, but there were also different paths in the acts and storylines for each other.
If you attached Sonic 3 to Sonic & Knuckles, you were presented a single game which consisted of the first 6 Sonic 3 stages, followed by the 8 S&K stages. The good thing is that you could play as Knuckles in all the Sonic 3 stages, unlocking the new paths in the first 6 levels and following a different storyline from the beginning as well.
This could seem like a big plus on Sega's side, but digging a bit into the original Sonic 3 game it was clear that S3&K was meant to be a single game that got split later for reasons I don't know (maybe greed or tight schedules, or both). The fact is that if you do the level select code in Sonic 3, you not only can see the names of all the S&K stages, but you can also listen to almost all its music as well. And, with the debug code, you can access the Knuckles areas and see some animation frames for Sonic and Tails that were only used in S&K stages. Add to that the cheapness of the Sonic 3 original ending (compared to the ultra-epic S&K ending), and the fact it only had 6 zones (while Sonic 2 had around 10), and that's why I felt quite disappointed 10 years ago
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Surely the separate release and the lock-on thing meant some added bonuses, the possibility of playing with Knuckles in Sonic 2 being the most notable of all. I would also bet that those Hyper Sonic and Hyper Knuckles thingies, or the doubled emeralds in the second half of the game, were added later because they didn't made much sense. Anyway, despite this bonuses I would have preferred Sega to release what would have clearly been the greatest and biggest Sonic game to date.
