It depends on what you want to go for in the game.

If you want a pretty much guaranteed skill shot, you can just plunge to the top lanes. It advances your bonus multiplier, which is nice in of itself. End of ball bonus can be huge, though you'll have to build it up enough with a long ball (playing a multiball that always diverts the ball into the bumpers when you make a loop can be helpful in doing this).

Super skill shots are risky but are valuable; you can complete the 3-bank in front of the saucer easily with one shot, which is helpful if you're focusing on destroying saucers. You can also make one of the main shots to instantly complete its line of inserts for Total Annihilation (which can be huge if you play it well). But like I said, these can be considered risky to go for because you have the potential to flat-out miss the shot that you're going for and wind up with nothing. You kind of get some pressure on you because the super skill shot is timed, and will thus go away if you take too long to successfully make anything.