Is it ultimately due to the Wii CPU being not powerful enough? Just curious.
Yes ultimately it is the Wii's hardware not being powerful enough. So every change makes it difficult. For example the change I made is perfect for Jikkyō Oshaberi Parodius. In the current version the FPS drops dramatically and with the change it is stable around 58 /60. But it seems like it is impacting Super Mario RPG and Kirby's Dreamland 3 but it is not. In the end it is the limitation of the hardware. In Snes9x they don't use hacks for these two games because on the computer you have more resources.
For example the new fork Snes9x RX is nice but it's build with an older core where some issues with games occur other then the issues in Snes9x GX where some of the issues are fixed but other issues arise. So also with that there is no perfect. And because the core difference not all code is interchangeable. For example Robocop vs Terminator is not working correctly but what has been done is a complete overhaul of the core to get that game and some other games depending on the same change to work for example daffy duck.
What is nice is that when Snes9x changes we can backport it now in Snes9x GX because the code used is almost identical.