While i'd say that the combined full version of Sonic 3 that is Sonic 3 & Knuckles is the outright best i'd also say that taken on its own merits Sonic 3 is still right up there, it may be short but it's pretty sweet all the way through and I prefer it to the "& Knuckles" portion of the duo.
To kick things off Sonic 3 casts away the opening zone look that Green and Emerald Hill shared, no chequered ground here on Angel Island, instead the lush jungle paradise gets burst into flames shortly into the first act which is not only a surprising way to take things for an opening act but it really lets the visuals show off, Sonic 3 is a much more cinematic game than those before it but not enough that it's intrusive, it's a nice touch that also lends itself to creating a link between all the stages you visit. I tend to like it more each time I play it which is worth something.
The second Zone Hydrocity dares to challenge the notion that water in Sonic has to suck, Hydrocity creates a watery environment that's relatively safe with the new bubble shield removing the need for air and deflecting certain enemy turret shots, currents wash Sonic through underwater passages and soon enough you're back on land zipping down waterslides and running at such a speed that Sonic sprints across the waters surface, the stage creates a neat bit of contrast, fast paced land sections mixed with the slower water sections and they manage to merge quite well, once you start getting a bit tired of the pace of one the game will switch things around again. Act 2 has a memorable start with the killer crushing wall, its' perhaps a bit too much for this early portion of the game but I like it. Going back to the slow and speed juxtaposition even both stages themes take a slower and faster version of the similar melody.
Marble Garden might be viewed as the weakest link of Sonic 3, there's certainly some flaws to this place, it's almost like it's designed to have as much speed halting enemies as possible with the giant ball and chains, faking you out with fake spike traps, those blasted grasshoppers and even the slowing mud that populates the stage, I don't have much to say on this zone but the later part of Act 2 is rather dynamic with the ruins and earth itself all rumbling in such a way that the layout is ever shifting in an effort to crush Sonic. The boss also makes use of the duo dynamic of Sonic and Tails.
Carnival Night falls victim to the infamous barrel trap that holds a lot of weight when it comes to peoples memories of the zone, but this zone is more than just a poorly explained barrel, it's one that pushes the chaotic nature of its predecessors (Spring Yard, Casino Night) even further with more varying stage elements and more bouncing around. Effectively this zone is a mess but it's a mess in the best way possible, even when it feels like you might be completely heading in the wrong direction you will eventually reach your destination. Act 2 has an interesting visual shift midway through when the evry interfering Knuckles knocks the power out, I probably prefer Casino Night to Carnival Night but get past that barrel and it's not a bad zone.
Ice Cap actually starts with an act i'm not too fond of, Sonic snowboarding holds zero gameplay, it's just a cool visual, the stage takes place in a cave that incorporates the same magical technology that Sonic 1's labyrinth employs, that being looping areas of map that keep going around and around until you get Sonic down the right path, so no i'm not so big on act 1. Act 2 however is a great recovery, bursting out of the cave and onto the exterior, Act 2 is a stage that really rewards you for platforming up to the top route and keeping out of the cave areas.
Lastly we've got Launch Base, since it's not truly the final zone of this saga it's not really that difficult, I find it pretty fun regardless and it's a different take on the usual Robotnik/Eggman tech fortress theme with a focus on exterior areas and even a quick dip in the wet stuff but never in a way that slows you down much, it keeps a speedy focus and doesn't lob traps every step of the way like scrap brain nor does it cause the grief that Metropolis seems to (personally i'm fine with that zone).
So that's not a huge selection of Zones, Sonic 2's greater wealth of stage content is enough to possibly still stand above Sonic 3 but then again Sonic 2 has Sky Chase and Wing Fortress so maybe I do prefer Sonic 3 on its own.
The save mechanic is much appreciated, Tails is fully playable with his own unique paths increasing the replay value, music is consistently funky, the visuals are bolder, the stages more flashy and dynamic, the shields open up more variation in how you can approach sections.
Basically i'll stand behind Sonic 3, bolt on Sonic & Knuckles and it gets stronger still.