The prototype music caused a huge stir when that prototype was released. People always assumed that the Sonic and Knuckles Collection music on PC was specially arranged tracks which replaced the music tracks that were composed by Michael Jackson (uncredited) and his team with samples from other artists. The suggestion was that the tracks were too complex to be reproduced by MIDI and so were replaced. Turns out those tracks were intended before their involvement. The the same tracks were replaced in Sonic Origins and it turns out they could not licence the tracks from everyone involved so the prototype music was remastered.

Sonic Origins would fix the "abrupt" ending of Sonic 3, by adding the Title Screen of "Sonic & Knuckles" but without the title characters, to show the Death Egg crashing into Lava Reef zone.

Fun fact: the initial commercials for Sonic 3 said it was "Twice as long as Sonic 2". But later commercials modified it to say "Zones twice as long as Sonic 2" instead.

"Here's what it sounded like in Sonic 3 standalone:" (ring scattering sound) (ring scattering sound) (ring scattering sound) (ring scattering sound)

Sonic & Knuckles would basically include Patches for Sonic 2 and 3.

Michael Jackson not liking the Genesis sound chip being used as the excuse for his removal from the credits never made any sense to me. There's literally a game about Jackson featuring his very own music on the Genesis, and he's in the credits. Furthermore, he would have been familiar with the console's sound already by the time Sonic 3 was being developed, so if he didn't like the sound chip, why the hell would he want to make music for the game?

Jon Buton of Traveller's Tales, Game Hut, and Coding Secrets said the structure and complexity of the lock-on code indicated that Sega probably planned to split the games earlier than the popular narrative suggests. His team coded Sonic 3D Blast and he worked on Sonic R, Mickey Mania, Toy Story, and more during that era.

I had Sonic 3 when I was I kid and it looked like a nice game in length. I never felt like saying: "damn, this game is too short and feels incomplete". We didn't know about the story on the backstage. It was a great experience with long levels and themes. What a surprise was to know months later about Sonic and Knuckles. Only years later we knew they were supposed to be one single game, but it didnt' erase the experience we had before.

The MJ thing doesn't make any sense. He would have known what the chip sounded like before agreeing to the project. He also allowed his name and music to be licensed for the 1990 Mega Drive/Genesis game Moonwalker. To know what the chip sounded like, he could literally listen to his own music being played on the console before deciding to write any music for it. It makes more sense that he got his name taken off the project by Sega because of all the rumours that were surrounding him at the time.

The silence between acts in S3 was kind of eerie. It added a feeling of tension as you waited to see what the next part was.

Youtube's autogenerated subtitles thinks your name is Poer

Sonic 3 & Knuckles was one of my favorites on the Genesis as a kid. I remember the lock-on technology marketing from Sega definitely got me excited. I'm actually glad Sega wasn't able to do the isometric game they originally wanted as I doubt it would have held a candle to Sonic 3 & Knuckles if Sonic 3D Blast is any indication.

As a kid, I thought Sonic 2 was the better game, but I've come around now to liking Sonic 3 & Knuckles a little more. In fact, I'd argue that Sonic 3 & Knuckles might be one of Sonic's best entries maybe outside of Sonic Mania.

One of my favorite aspects of Sonic 3 and Sonic and Knuckles was the transitions between each world's made sense. But the problem is is that when you beat the last level of Sonic 3 it just dumps you into mushroom Zone with no context of how you got there from launch base

The complete game was later ported on Sonic Mega Collection on GameCube, Classic Collection in Nintendo DS and Origins in Nintendo Switch.

I still vividly remember the hype behind Sonic 3's release, being a huge fan when the franchise was brand-new as I was reading the comics and watching the cartoon shows on TV.

I loved the hell out of the game even though in hindsight it was a little shorter, but there was plenty of replay value looking for all the emeralds, exploring around for shortcuts, and also playing with Tails' "new" flying ability which we couldn't do in Sonic 2.
The announcement for the then-upcoming Sonic & Knuckles felt like an expansion of what was already a fun game with the added bonus of being able to play as Knuckles outside of 2P competition mode. With Knuckles exclusively being able to go through paths I always wondered about like the three stone walls before the first actual miniboss fight in Angel Island. Back then, I had no idea Sonic 3 was INTENDED to have all the levels that Sonic & Knuckles also had, but to kid me, it felt like a surprise bonus extra to what was already a fun game... and honestly, it was a bonus within a bonus, because Knuckles was also surprisingly playable for Sonic 2... and optionally Blue Sphere with endless levels if you wanted to be a masochist and do that for as long as you wanted.
Kid me humored the thought Knuckles could be playable in various other non-Sonic games, but then we've got romhacks for that nowadays :P
Though the changes in music from Sonic 3 to Sonic & Knuckles are personally better... The original miniboss theme sounds more like a theme song for a joke character, while the invincibility/Super Sonic tune was repetitive as holy hell to the point I eagerly awaited for it to wear off so I can listen to the better background music again. The other changes to the levels you brought up I also noticed as a kid, I feel they were anti-frustration measures since those old traps were annoying and unfair.

As for the changes in Sonic Origins, as an old-school fan, I kinda don't really mind them? If it plays close enough to what I remember as a kid, it's good enough to me. The addition of Drop Dash added way more options and fun to replaying those old games... including and especially Sonic 1 which is kinda sluggish compared to 2-onward when they introduced the Spin Dash and such. Also infinite lives, I'll never miss game overs and continues, it's such an archaic thing nowadays unless someone wants the old-school difficulty.
The changes in music I also begrudgingly understand why they did so, the MJ estate being tricky to work with considering how big he was and personally, I don't mind the changes for Carnival Night and Launch Base, as I also remember hearing them for the first time in the old PC version, which we now know were the prototype music before MJ's involvement... The hardest one to accept is Ice Cap which we now know was taken from Brad Buxor's band The Jetzons titled "Hard Times", which was catchy as hell... But I guess those old songs can be modded back in on the PC version, just sucks for those on console... at least we have mp3s and older rereleases to still enjoy those tunes... And I suppose making a deal with Dreams Come True for the music from the first two games are easier to deal with in comparison.

The first DLC prototype???? Sonic really was ahead of the competition!

The interesting part is in sonic origins we got stuff  many years later like playing knuckles and even tails in the original sonic game.

Didn’t know Sonic & Knuckles was supposed to be the second half of Sonic 3 back in the day, just thought of it as an expansion pack.

Open up the S and K cart. It has a sonic 2 rom chip inside. Thats why you cant play sonic 1 cause there is no rom inside for it.

The mini boss music in Sonic 3 standalone can be changed if you manage to almost drown and them come out of the water.

I had Sonic The Hedgehog 3 as a kid but not Sonic & Knuckles. However, in Sonic Mega Collection for the Nintendo GameCube, you can actually play Sonic 3 & Knuckles and Knuckles in Sonic 2. But you have to unlock them.