I just re-tested again with the newest drivers, Windows build, etc.
System:
Intel 3570k overclocked
16GB RAM
NVidia 660 GTX
Windows 8, 10, Linux with compositing disabled (tested all 3)
Dolphin build 6554 (the netplay build)
Project M 3.6 Beta
Using official WiiU GC adapter, official controller
Wii motes off in Dolphin
V-Sync is off, fullscreen on at native resolution, other config settings as per netplay guide
Low latency monitor (like I said, I measured it at 1 frame of lag in another game). I know the difference between lag and response time.
Same results as before. 4-5 frames of lag. I've been mentioning this here and there but no one seems to believe it. If I get around to testing more random systems, I'll make a real thread with the results. I'm familiar with measuring input lag, as my Master's thesis is on input lag. I've measured both the frames required for a jab animation to start when hitting A, and the pause screen to start appearing when pressing start.