It sounds like I'm having a similar issue to you. I've outlined some notes below, with the hope this raises potential solutions. I do not think it is an issue with an update to NewPipe because I've been using version 0.28.0 for months without issue. However, I cannot say whether it is an issue with the latest GOS update itself, if the GOS update exposed a weakness in NewPipe that was being masked prior, if YouTube is detecting videos playing back in NewPipe and throttling them, or another issue. I suspect it isn't YouTube throttling the video though because I haven't seen any relevant reports on the GitHub for NewPipe.
Symptoms:
First started less than 1 week ago.
Videos in NewPipe stutter during playback. Will stutter periodically for 10 s, go back to normal, then repeat. It is similar to when you hit a CPU or GPU heavy area in a game.
The audio is not affected.
Happens on both WiFi and mobile data.
Videos play back fine on YouTube in Vanadium.
Devices affected:
Pixel 8A, GOS build 2025121701, NewPipe vr 0.28.0
Pixel Tablet, GOS build 2025121701, NewPipe vr 0.28.0
What I've tried (no improvement):
Reducing resolution and framerate.
Clearing storage and cache for NewPipe.
Deleting and re-installing NewPipe.
Changing exploit protection settings for NewPipe.
Turning off and on battery saver.
Ensuring devices are fully charged and trying with the devices plugged in.
Wiping and restoring the device to factory setting (Pixel Tablet only).
Happy to do some testing and playing around with settings.