They are both really good games. I also have issues with both of them.
SM. Doc Ock all day. Ignore the rest of the game, take what comes to you as you work on Doc Ock.
PotC. Multiball stacking is king. Other than that... chopping wood.
There is a reason why you don't see either of these games in many big tourneys. They have to be nastified to the point of being whisper tilt lightning flipper crippled to keep them from going on forever. Between the two, I'd go with SM just on the fun factor. However if these games are for home game room fun... get them both and see which one you like the best.