It is very, very, very likely (as in, I'm 99.99% sure of this, I'm just waiting for a specific dump to come out (which has been found) to be able to present as absolute proof) that the 8-bit Sonic 1 port is based off of a very early version of Sonic 1 for the Genesis. What is very likely to have happened is that, once Sonic Team had stopped iterating on core gameplay and level tropes (i.e. after their initial CES appearance with the non-interactive demo), they likely had a meeting with Ancient to get on the same page then didn't communicate after. Between that period where Sonic Team met with Ancient to present what they thought Sonic 1 would be, and when Sonic 1 on the Genesis ultimately released, a number of changes occured that didn't get reflected in the 8-bit port.
So when you look at the 8-bit version of Sonic 1, you are looking at pretty much a split timeline of development. Lots of things in the 8-bit Sonic 1 port resemble parts of the unseen prototypes of the 16-bit version of Sonic 1. A repost of an old topic with a little bit more info:
First - Bridge Zone contains the Yadorin badnik. We know that this badnik was originally supposed to be in Marble Zone. Similarly, Sky Base Zone contains both Bomb, and the special version of Unidus from Labryinth Zone which does not shoot it's spikes - both enemies from Star Light Zone. Now, the special stage in Sonic SMS doesn't contain any badniks, but Spring Yard Zone in Sonic MD recycles most of it's badniks save for Arma.
Second - The Special Stage in Sonic SMS is largely useless. It exists only to give continues. In Sonic MD, the special stage is there to give you chaos emeralds, but since there are emeralds in the stages in Sonic SMS, it renders the Special Stage unnecessary. Now, the Special Stage contains a lot of unique gimmicks which are similar to Spring Yard Zone - most noticeably the bumpers. These appear only in the special stages in Sonic SMS. My personal belief is that they were originally coded for spring yard zone, and reused later for unknown reasons.
Third - the art of the zones are very similar to existing zones, as are their tropes. Bridge Zone obviously is the most different, but a simple change in the palette makes the zone look a lot like Marble Zone:
Bridge Zone and Marble Zone also share similar objects, such as this platform:
Perhaps more obvious is the similarities between the special stage and spring yard zone:
Obviously the Special Stage features what is largely considered the defining feature of Spring Yard Zone - the bumpers. But at first glance it seems to share little else in common with the final Spring Yard Zone. The background is completely different, especially... until you compare it to sparkling zone:
Suddenly the two zones look remarkably similar, especially the background, which features the same dark shade of blue and sparkling stars.
Lastly, we have Sky Base Zone, which borrows a lot from Star Light Zone's industrial highway motif. First, you'll notice that SLZ's yellow-and-black caution color scheme is copied a lot:
That yellow-on-black design is used quite a bit in both stages. The main pattern in the level - industrial squares with lots of rebarbs sticking out, is also used in both zones:
It's a bit harder to see because of the flashing palette in act 1 of Sky Base Zone, but the structures are incredibly similar. Even random objects in the background are similar, like these glowing lights and cones:
Now, even though it's included, I've always felt that labyrinth Zone's background in Sonic SMS was similar to Labyrinth Zone's background in the Sonic beta, with lots of black and smoothly blended sections of background:
Fouth - Sonic sings in the ending, and the title screen is black. This is the most obvious similarity, since we know both were a staple of early versions of the game. Magazine scans have shown that early versions of Sonic MD had a title screen similar to Sonic SMS:
and, more interesting, we know that at one point very late in development, Sonic MD had a robust sound test mode featuring a fully animated band. Concept art shows that Sonic was the singer, and we know this was removed extremely late in development to make room for the "sega" soundbyte:
Sonic SMS's ending shows Sonic, fully animated, "singing" the end theme song. I've said many times, I believe this is the last remaining piece of that soundtest mode:
