Sleeping on it, part of the answer's pretty obvious: RAM and ROM cost.
The SMB1/Zelda/Metroid etc tile map were this big:
Moving to 3 bit color would have shaved 33% of the tiles off of the sheet, using the same amount of memory. (And using more was impossible at the time, when they wanted this thing to be as cheap as buying two toasters.) Woulda been almost SNES-level good looking if they got it working tho.
(The SMB1 tilemap always makes me feel like looking at the work of an illustrator/animation guy.
Naturally they'd want to invest most of the map into the 1 thing the player will be looking at constantly. It's all very clearly Pop-eye, the inspiration shines through.)
I was asking here about the game's save system a while back
I 'memba. I'ma assuming this is on CD, so a dead card battery wouldn't be the culprit.
Thinking about it now, if there was something unique to say about the save system the FAQs at GameFAQS would have said it, but my googling suggests there wasn't anything there. I think this may be a defect of some kind, or some wonderful issue unique to you and this particular game.
Let me tell you a couple tales of fucky hardware stuff. They'll sound like made up BS, spooky copy-pasta attention seeking nonsense. Like seeing a UFO or bigfoot. They are 100% true, they're not the mandala effect, they weren't brain hallucinations. They wouldn't have been this consistent.
My Sega Genesis's AV cable was slightly cut, and repaired by wrapping some electrical tape around it. The game Shining Force has a cheat code you can input to enter a battle select menu. The code is rather complicated and time sensitive to put in. For some reason it activated a couple of times while I was doing stuff with the AV cable. The code requires hitting the reset button, pressing some buttons at certain times. I had no idea it existed, I wasn't touching any buttons, and I think it entered the battle menu at a time it shouldn't have been allowed to.
Naturally, when I tell people this no one believes me. (I guess this sort of thing isn't literally impossible, which is why some were willing to give some credence to that "human element" Dragster, but only on his machine. But I'm telling the truth damnit. ;_;)
Another is that time the sound "fell off" of some of my Firefly discs. Played fine for weeks, one day the audio just stopped working. Other discs worked fine.
We tend to romanticize hardware a bit, but they're fallible imperfect beings made of coarse matter as well.. one or two bytes dying or flipping weirdly somewhere can have strange outcomes in digital systems. One stupid bit being wrong in your save file might make the game invalidate it completely. One number being wrong oftentimes doesn't hurt much in most instances, until it causes a disaster.
It's... feasible that your save memory is working fine except for one corrupted byte that only becomes a problem with this game. ... one way to narrow it down I guess is to try some other external form of memory, if your system supports a save card or something. Dunno if those will be littered with dead batteries or if they have some nonvolatile state options, I'm not familiar with the hardware which is why I didn't say anything before.