And that stutter occurs with either ubershader settings regardless of whether you use Direct3D 11 or Vulkan?
You could also try the "Asynchronous (skip drawing)" option which can cause various weird graphical issues but is also supposed to be stutter-free.
Otherwise I would check your CPU utilization － are you maxing out one of your CPU cores and/or not hitting a constant 60fps? If so, then there's still a few things you could possibly do that may alleviate that. (note that Dolphin only really heavily utilizes 2 cores, so with a 12-thread CPU your total utilization could appear to only be 15% even if you're CPU-bottlenecked).
You could also try the "Asynchronous (skip drawing)" option which can cause various weird graphical issues but is also supposed to be stutter-free.
Otherwise I would check your CPU utilization － are you maxing out one of your CPU cores and/or not hitting a constant 60fps? If so, then there's still a few things you could possibly do that may alleviate that. (note that Dolphin only really heavily utilizes 2 cores, so with a 12-thread CPU your total utilization could appear to only be 15% even if you're CPU-bottlenecked).
Dolphin 5.0 CPU benchmark
CPU: Pentium G3258 @ 4.5GHz 1.24v
GPU: Intel integrated
RAM: 4x4GB Corsair Vengence @ DDR3-1600
OS: Linux Mint of some variety + [VM] Win7 SP1 x64
CPU: Pentium G3258 @ 4.5GHz 1.24v
GPU: Intel integrated
RAM: 4x4GB Corsair Vengence @ DDR3-1600
OS: Linux Mint of some variety + [VM] Win7 SP1 x64