Stenzek changed the license because he had a meltdown last month when PCSX2 changed it's license from the LGPL to the GPL (which is allowed by the LGPL; there's nothing dubious about making this change)[1] for... some reason. In response, he threw a tantrum and closed all his open PCSX2 PRs, effectively quitting the project[2][3][4].
RetroArch is a plague on the emulation community, but that's not why Stenzek relicensed his emulator.
[0]: If this is actually incompatible will largely depend on your views how the GPL interacts with dynamic linking. Don't just repeat the FSF FAQ, look for other legal opinions not written by free software advocates.
[1]: https://github.com/PCSX2/pcsx2/pull/11648
[2]: https://github.com/PCSX2/pcsx2/pull/11315
Pretty sure it's because he would be "forced" to open-source Aethersx2 (which is an android port of pcsx2).
It would only prevent him from using code added after the switch to GPL, which is not a problem because AetherSX2 ended development long before PCSX2 switched to the GPL.