It's more fun to play the modes, but if you really want the best score, you're better off skipping most of them and letting them time out. The ones I usually play are Rescue, Asteroid Threat, and Time Rift -- they are easy because they light every single shot. Worm Hole and Search the Galaxy should be skipped because they require the upper flipper shot, which is both a low percentage shot and a major drain risk. Yes I know Search the Galaxy has multiple artifacts up for grabs, but it's just not worth losing a ball over.
Battle Simulation has an extra ball if you make 6 consecutive shots, but missing sends the ball out of control and bricks off the Neutral Zone often go STDM -- play at your own risk.
Holodeck Simulation (video mode) is very important - you can get an extra ball and an artifact, plus about 130 million points if you memorize the correct pattern. If you don't care about points, squeeze the trigger and hit the right flipper button at the same time and you will play poker against Riker instead (although it's not worth much).
One 'easy mode' setting I have turned on (mostly for guests) is unlimited Lite Lock on skill shot. So if you want, instead of starting a mode or Warp 4, you can lock a ball on all 3 of your balls for a guaranteed Borg Multiball on ball 3.