same boat as you OP
Playing mother 3 (at least I want to)
gpsp - full fps however theres a freaking line through the screen which annoys the fuck out of me, also random crashes.
mGBA - rarely full FPS - usually around 45 to 55 which is definitely playable but not to my liking. However it never crashed on me and I love the interface.
everyone and every thread pointed me to gpsp and it sucks - I don't think they're even working on it anymore (I heard they recently wanted to continue or have started)
it has tons of setting options however one wrong click in the settings crashes the app....so I spent a good 2 hours trying to get the perfect setup to play mother 3. no luck btw.
injecting means no save states and pretty much featureless - no thanks