My understanding is also that prestige is based on the highest on your team of 6 (whether it enters the battle or not) vs. each defeated target.

I can't personally confirm that, though, because all the fighting I've done since the change has been, for a variety of reasons, with my whole team lower CP than the lowest defender.

https://www.reddit.com/r/TheSilphRoad/comments/56xd8r/psa_prestige_gain_is_calculated_based_on_the/