What's wrong with the save system? It has the hard save that sends you back to the start of the cycle with your major items intact (And rolling around the field as a Goron for a minute or so will restock all your items) and it has temporary saves at strategic locations if you're in the middle of some task that you want to resume the next time. You can even put your rupees in the bank so you don't lose them.
I think the only change I'd of made on the N64 is make the temporary saves act more like Ocarina of Time's standard saves. Allow you to save on demand via the menu and return you to the last entrance you went through. I don't see why they had to restrict it to just those owl statues since it can be a bit of a pain if you're saving mid-dungeon. Sometimes Nintendo can be too clever for their own good and I imagine this was one of those instances.
With the 3DS and what I imagine is the inevitable follow up to Ocarina of Time 3D, I would hope the temporary save would put you back right where you left off thanks to the progress of technology making such a thing easier to impliment than back in 2000 so no back tracking in a dungeon is necessary to reach where you had left off.