It depends how much you need to prestige.
Sometimes there is an outlier at the bottom, with very low CP, with those above it in a tight CP bunch. In this case I will ignore the bottom one, and set my team up with the next few in mind - then kill the lowest fast and prestige against the rest.
Otherwise, if the CP are well bunched, then I set up a team that can take 3 or 4 in a row - hopefully not hitting a Blissey, and go max prestige as far as I can...then rinse and repeat.
It really depends on what is in the gym. If I have to I will just max prestige against the bottom mon...and then get out and go again - but this is my last resort.
