Sonic Team gives more insight on why Sonic 3 was split into 2 games

Coming from a Game Informer interview with Sonic Team head Takashi Iizuka...

"We did 1 and 2, but the plan going forward to 3 was that we really wanted to hit a home run. We wanted bigger maps multiple times larger than Sonic 2, but we also wanted to have more maps; we were having more maps that were also bigger and take more time to develop. The cartridge sizes were limited in space, so we were finding out that not only did we have these obligations to get the content out at a certain time, but we also couldn't get this massive game that we wanted to make onto the space that the cart would allow."

This lead the dev team to split the title in half, but they didn't want the games to feel like two separate experiences. This lead to the lock-on tech that was created for Sonic & Knuckles.