Why not use another emulator?
That's sort of what I'm currently in the process of doing. I used to use Nestopia until I started running into some minor sound glitches with recent hardware. Forget for a moment that I'm trying to adjust the aspect ratio, but I can't find anywhere in Nintendulator that will even let you change the resolution. That seems like it would be a pretty glaring oversight. All you have are the few multipliers in windowed mode, and nothing for fullscreen. It's hard coded at 640x480!
Please realize I am not complaining. I'm simply trying to give this emulator a chance. I heard it has very accurate emulation, which it seems to, and I do not experience any sound glitches with it. Rather than make some random choice, or blindly follow the one I've always used in the past, I'm trying to make a somewhat educated decision here by testing a variety of emulators. I've arrived at Nintendulator, and I'm wondering how to tweak some very basic video settings. If this is not possible, then I will brush one aside and continue looking, but I want to make sure I'm not missing anything. I don't want to discount an otherwise good emulator for something that may easily be fixed.