Hmmm, not sure what you mean by basic? You mean like the command normals: B+BP, F+BK, B+FK, stuff like that.
In my opinion using your setup seems really difficult. You have to re-finger between each command normal and each special move. And do you ever get confused?
Also, could you state which pad your using.
As for playing entirely on the analog stick, I suppose its possible, as it would be like the stick on an arcade stick. MK9 doesn't require diagonals, so pressing the direction buttons is much easier.