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The 3DS might not be fast enough to handle it at constant full speed without extensive modifications to the core (which might end up sacrificing accuracy), and at that point, using a less accurate emulator like FCEUX would make more sense, since the focus is speed more than accuracy. I think that's what we're trying to find out while Steve improves the speed via GPU rendering. Once that stone's had the water squeezed out of it, then we'll see where that leaves us.
Yeah, most of the speed issues are likely in the emulator itself. I ran it once with graphics disabled and it still ran a bit slow. It's likely a need for optimization in the NES PPU and/or CPU code.