Yesterday night I played with the screen blit function to handle the alpha channel in a more efficient way and introduced a frameskip of 1 (like the way the PSP version does).
This way, with a 2x zoom and a sync cycles value of 16, I doubled the speed and now it can reach about 50 FPS. The perfect value should be 72 FPS, but now the speed is not bad at all.
I introduced also an option to chance the screen resolution (1x and 2x) and it's zoom value (none, fit height, stretch to full screen).
I tested this only on Citra, but tonight on a real o3DS I expect that with an 1x resolution (zoomed to fullscreen with HW rendering) I could gain some more FPS.
So now I have enough speed to work on sound.