There’s currently a “frame stuttering” bug in mGBA that has been bedeviling the developer for a while now: Visual stuttering and frame drops regardless of settings · Issue #2199 · mgba-emu/mgba · GitHub
I was getting stuttery framerate too; most of it went away after I lowered “Settings - Audio/Video - Audio buffer” to the minimum setting, 512–which is also supposed to minimize input lag.
Another work around for the stuttering issue is to set “Display driver” on that same page to “OpenGL (force version 1.x)”; this eliminated the last of the stuttering for me–it wasn’t really detectable in Sonic Advance, but was pretty obvious in F-Zero Maximum Velocity.
So, this is good! It fixes the janky feeling I’d associated with GBA emulation to this point–because Visual Boy Advance-M has it–or something very like it–as well.
Unrelated, in mGBA I’ve set “Settings - Enhancements - OpenGL enhancements - High-resolution scale” to the max, 16x (“3840x2560”); this makes Mode 7-style FX, like the ground in FZMV, render in high resolution rather than GBA base resolution, which makes a big difference; does not work in the “force” renderer though, and there’s no “force” renderer in the Enhancements page’s drop-down selection list (so Enhancements run through a separate renderer, interesting = o).