Hello all, a quick PSA :)
The lr-mupen64plus-next core got updated some days ago and now is defaulting to 640x480 resolution for new installs. This resolution is a bit taxing for humble devices such as the RPI3 or less, so is strongly recommended that you set the rendering resolution to 320x240 (as it was previously the default) for these devices. Perhaps this is not necessary for RPI4, you have to see for yourself.
This can be done after starting any game and going to the core options menu in RetroArch.
It is important to note that this is not a RetroPie change, but an upstream change. We decided to not change the upstream defaults therefore it is your responsability to change this setting for your own setup.
If you had the core previously installed, the new defaults will not apply because you already have the previous resolution set in your core options.