I generally prefer using 2nd for jumping, but as long as there's no button to press to run. Otherwise, I prefer jump to be 2nd. I find it hard to run around when running uses ALPHA and jumping 2nd, because I am used to horizontal/diagonal controls for mario games. (Like the NES). In Metroid II: Evolution, the only reason why I used up to jump is because xLIB getkey only multi keypress support was up-rigth, up-left, down-right and down-left, nothing else.