It won't necessarily be a good experience. For one, the frame rate is ever so slightly off, leading to very stuttery movement which really hurts my eyes when I try to play Mega Man 3. Since it is emulated, you never know if you're going to run into issues or not, and this is not a very accurate emulator.
Second, the palette will never match exactly to what the original NES outputted since you have to simulate what was originally YUV to RGB (same goes with an RGB modded NES and PC emulators) by faking it with a palette. This is a non-issue to most people, though.
Third, Neon64 is not an updated emulator (nor is it made by Krikzz), so do not expect any support.
Will it be exactly the same as an RGB-modded NES? No, because the emulator is not 100% accurate. Will it look close? Probably.
As for me, I'll stick to using my NES controller with my PC hooked up to my TV via transcoder, and I'll just use Nestopia UE via RetroArch until I get an NES + Everdrive N8. I'll probably stick to an unmodded NES as well unless there's a way to output something with native YUV, such as YPbPr using the original palette.