For example in the usual scum build of Wedge, Luke, Biggs. I'll leave Luke till last. Against the high intercepter list I'll go for highest PS.
This is usually a bad idea because PS doesn't identify the correct threat. For example, in the rebel example Luke is an incredibly dangerous endgame ship (especially with R2-D2), while Wedge is fairly easy to kill. So you might be better off taking Luke down while you still have the ships to put concentrated fire on him, and dealing with Wedge later. After wave 4 arrives you might even need to gank PS 3 Tarn Mison as your absolute #1 priority because his R7 droid makes him one of the hardest ships to kill 1v1.
And then of course there's the position issue. Fel might be the highest-PS threat, but if your opening maneuvers gives you a better position to chase down and kill Phennir then you'd be making a game-losing mistake if you gave up that opportunity and went for the harder target. Or you might have a case where the low-PS ship is at range 1, while the high-PS ship you want to kill is at range 3. In that situation you're usually better off taking the sure kill instead of throwing uncertain shots into the high-PS target you've declared your priority.
In short, don't go into a game with rigid rules about which ship is the priority target, always assume that you'll take the shots you're given regardless of what you're "supposed to" kill first.