Best Level Ever: The Special Stages from the Sega Saturn version are a fan favorite, being a vastly improved version of the Special Stages from Sonic 2. These stages are rendered in true 3D and have more elaborate features like springs, gaps, and upper/lower paths. On top of that, they are arguably less headache inducing than the Sonic 2 Special Stages.
Some elements, such as the upper/lower paths and the animation sequences were retained in the Sonic the Hedgehog 4 - Episode II Special Stages.
The Sega Genesis / Mega Drive renditions may be very straightforward, but there's a welcome simplicity compared with the much harder, complex Special Stages in 2 and 3.
Ear Worm: Despite not being one of the most popular Sonic games, it has one of the better soundtracks. Gene Gadget Zone in particular has music that's right up there with IceCap and Lava Reef as some of the best Sonic music ever. Two of the Mega Drive tracks (Green Grove Zone and Panic Puppet Zone) were so well-liked that they were later directly reused for levels in Sonic Adventure.
Goddamned Bats: The snowman Badniks in Diamond Dust Zone, which due to the isometric nature of the game are far more annoying and difficult to avoid/kill than any of the Badniks in Metropolis Zone. And in this game, you have to kill them in order to complete the level.
Good Bad Bug: In addition to the Classic Cheat Code activated level select, there's a second way to trigger it. As part of a kind of safety feature, if the game's brains get sufficiently mixed up that it tries to execute out of range code, it'll automatically skip to "CONGRATULATIONS. YOU HAVE FOUND THE SECRET LEVEL SELECT SCREEN!". The Mega Drive being fragile as it is, the easiest way to do this is to simply smack the console (especially during the prerendered 3D animation at the start of the game). It was either this, or simply crash.
You can also trigger it in emulators by opening a savestate of any other game while you have 3D Blast/Flickies' Island open.
Polished Port / Porting Disaster: The Saturn version substantially beefed up the graphics and palette with a variety of environmental effects, completely redesigned the Special Stages courtesy of in-house Sega of Japan developers, added analog control pad support, and provided a different CD-quality soundtrack composed by Richard Jacques. The major caveat - the load times were absolutely atrocious near the level of Sonic 06 (if not worse), leading to most online Let's Play videos to entirely mask it. The Japanese version released later marginally improves this issue and the PC port almost minimizes it altogether and even includes a basic save feature, but the former erases the cheat codes and latter removes the environmental effects and replaces the impressive Special Stages with severely downgraded ones widely considered even worse than those found in the original cartridge.
Collecting Flickies, mainly for slowing the pace of the game, as well as drawing importance to what is normally an afterthought in other Sonic games.
The Power Sneakers are basically worthless in this game—Sonic becomes even harder to control than ever, and it makes it very easy for him to accidentally plow into a nearby enemy or obstacle.
The Saturn port, for all of its merits, introduces another unwelcome change from the Mega Drive version—as the Tails and Knuckles set of Special Stages were merged, you can only collect one Chaos Emerald per act as opposed to two (going to the Special Stage a second time in an act will always give you a 1-up) which considerably drags out the pacing of the game, which was already bloated by the very tedious loading times.
Rusty Ruin isn't hard as a whole, but it becomes much more frustrating if you're trying to get to Tails or Knuckles. The big issue is that there are stone pillars obstructing your paths in both acts, and you have to use the Spinner devices nearby to destroy them—and the controls for Sonic spinning around (which makes him a lot faster than usual) are very slippery and liable to get you knocked into an obstacle by accident, robbing you of the rings you need to access the Special Stages. Act 2 also has a very tricky platform on an angle you have to traverse, and due to the games isometric controls, its very easy to miss the jump and fall down to the area below it, forcing you to backtrack all the way up and try it over again.
Volcano Valley is a very frustrating Lethal Lava Land with a ton of treacherous jumps over lava, chances are you'll end up getting hit and losing your Flickies more often then any other level in the game. However, if you can snag a Red Shield and hang onto it, the level is a piece of cake.
Gene Gadget Zone Act 2 is also a pain because of one section where you have to climb up a large incline by jumping between moving platforms and dodging enemies. This section is designed to loop around until you can manage to get all the Flickies, and chances are it'll take more than a few tries.
That One Boss: Most of the late game bosses can be described as this, but Volcano Valley's is the worst. Having to cross thin pipes in an isometric perspective with a rather slippery control over your character with lava and a dragon following you makes this boss a life stealer. This can be dealt with by attacking him quickly, but usually you'll end up getting hit and/or dying.