N64 emulation has also been very far from perfect. Actually I've found it downright unplayable, granted I haven't tried in a couple years.
I've not really tried N64 emulation in a couple of years* (I use the real console plus an Everdrive 64 flash cartridge, the latter is great for running modded/hacked N64 games), but when I have tried N64 emulation, it's often been problematic even if I do hit on the best combination of the right emulator, the right version of that emulator, the right plug-ins, and the right settings for those plugins.
I know there must have been good reasons for N64 emulators to have plugins and lots of options back when they were first released; different plug-ins allowed different people to work on improving graphical/audio/control-related etc aspects of the emulator, plus different people have differently capable PCs, so one PC could run a more accurate plugin, whereas a slower PC could be made to run a less demanding plug-in that was less accurate than the more demanding plug-in. But it's more than fifteen years since then so by now I'd have thought that N64 emulators would automatically know which plug-ins are the best for a given situation and so not need any user interaction but that wasn't the case the last time I tried N64 emulation.
Anyway apparently current emulation of the Gamecube and the Wii is better/more accurate than current N64 emulation.
There are two cycle-accurate N64 emulators in development (Cen64, and the N64 part of the emulator called MESS), which in theory will run every N64 game with 100% authenticity, but they are a long way from complete as yet. Plus sadly it's looking like Cen64 might have been abandoned, to judge from the lack of activity on it's official forum (see: https://forums.cen64.com/index.php), though it's not a major problem at the moment because probably no existing PC is yet powerful enough to run a cycle-accurate N64 emulator at full speed.
* The only time I do use an N64 emulator is when testing a rom hack of Goldeneye or Perfect Dark when I'm at work (and skiving off!) as of course I don't have my N64 with me then. N64 emulation of those two games (Perfect Dark, and Goldeneye) is very good indeed if you use the modded version of the emulator 1964 (from http://www.shootersforever.com/forums_message … f3cfa33a842c3f4). This allows the two games to have a much better frame-rate than they ever did on the real hardware plus it's pre-set to use the usual PC first person shooter controls (WASD keys plus the mouse). Unfortunately it's only guaranteed to run well with those two games as those are the only two games that were targeted by the two people who modded 1964 for this purpose (and they both had to put in a lot of effort to succeed).
Mupen64Plus with the SoftGraphic plugin is pretty nice. N64 looking properly filtered, filtered, properly sized screen buffers, Indy working, etc.
The last time I tried Muppen (or Muppen64Plus, whatever it was I tried) it didn't have a front-end, I take it that's been added now? It's great to know that Indiana Jones works now, Factor 5's games were notoriously difficult to emulate, and I was disappointed that the game was never released in the UK (the PAL version was completed but never reached the shops for some reason but it was leaked onto the 'net a few years ago so we can play it now).