You can save on the PC version.
As for the low framerates... THERE IS A FIX!
When you are in level, hold down M, and press Escape. This brings you to a hidden menu. On here you can enable Motion Smoothing. Why this wasn't on be default I don't know. Anyway that makes it smooth. If the colours mess up, just go to restart game on the same menu.
The Saturn version is still superior however. Did you see the PC version lacks all the transparent fogging and Rain effects on Rusty Ruin for example? Ripping out the fogging really ruined it for me, I thought it was really nice and created a nice atmosphere. If only the Saturn version let you save...