FPGA * is * emulation, and that doesn't make it somehow lesser just because of the stupid stigma around that word.
I'm going to quote old truths here because there's no point re-inventing the wheel - thanks elvis :
You can get an identical experience in terms of latency/lag from good quality, high accuracy software emulators that also use run ahead emulation as you can with MiSTer. Yes, that requires a somewhat complex setup and often powerful/expensive hardware (especially for something like BSNES in accuracy mode with run-ahead, but it can be done). A variety of objective frame tests, lag tests and MDFourier tests demonstrate that the accuracy is identical between FPFA and software emulation solutions with the correct settings applied.
So all these claims of MiSTer or FPGA in general being lag-free while software "can't" are simply quite wrong. However, I too prefer the MiSTer option for 2D, mostly because of the simplicity. As others have said, the ironically low volume of options are nice, and specifically for me I enjoy playing 2D games though a real CRT, which is very easy to get accurate modelines out of with MiSTer versus accurate software emulation solutions (i.e.: a powerful desktop PC, not an RPi which voids the accuracy and run-ahead capabilities for 16bit systems especially due to lack of power).
When it comes to later 3D, I actually have no great desire to have these FPGA emulated. I actually much prefer the benefits of software emulation to offer higher resolution rendering, virtual overclocking, improved load times, etc. Many 3D games already accounted for much greater latency due to animation frames, and very few require frame-perfect timing like 2D titles did. While MiSTer offers an excellent PSX core, I personally would rather play on DuckStation with highly customised video options per game. The one exception is the Saturn and PSX's library of 2D titles, which I do actually prefer on MiSTer on a CRT, or titles with pre-rendered backgrounds (Resident Evil, Parasite Eve, etc) which look wonderful on a low resolution CRT. So that's a bit of a middle ground.
But N64, for example, benefits enormously from something like ParaLLEl-RDP and accelerated 4X upscaling with all the blur removed that the console suffered from. Past that into the PS2 era, and PCSX2 is amazing. I have no want for FPGA clones of that era hardware. Same for Dreamcast, GameCube, etc. People hypothesise about future FPGA emulation of all of these, but I don't really care for the idea.
Anyways, long winded way of saying that "low lag" isn't really the killer feature of MiSTer. Moreso the sheer simplicity of "power on and play". Anyone who has had to try and troubleshoot emulators for non-technical people understand this (and even then, MiSTer is still rocket surgery for some).
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With 144Hz+ monitors and VRR/freesync/gsync, you can bypass tearing and 16ms limitations trivially. And this is rapidly becoming the preferred way to deal with emulation, not just for latency, but also for odd refresh rates (arcade games in MAME, for example, that are all over the place).
It's entirely possible to run-ahead emulate your way to unnatural latency numbers that are lower than real hardware. But again, you really don't want to outside of an academic exercise. Plenty of examples of folks who have done it. If you want to try for yourself, start on something really light weight like NES or simple Z80 based system emulation.
The irony of course is that you need some pretty expensive hardware to do so on complex multi-chip hardware like SNES. And again you do need a decent monitor. If you're emulating because the cost of original hardware is too high, it's kind of moot to go and buy a many-thousands-of-dollars system and screen to do it. Even with recent silicon shortages and price hikes, things like MiSTer offer a pretty decent way to get a consistent experience across a wide range of systems without breaking the bank.
But even then, if you've got a crap monitor, you may be forced with MiSTer to a 2-frame buffer. I have mine connected to a 60Hz consumer CRT via analogue out which is great for mainstream consoles, but no good for weird framerate things like GB/GBA, ao486, certain arcade titles, etc (all give a stable picture, but with obvious tearing). An analogue-adjustable-vsync arcade monitor would be nicer, which I have access to, but need to set up. Likewise my VRR capable OLED would be fun to test too, but is in a different room to my MiSTer setup.
Supporter of PicoGUS, PicoMEM, mt32-pi, WavetablePi, Throttle Blaster, Voltage Blaster, GBS-Control, GP2040-CE, RetroNAS.