I generally do dodge most of the time, especially the first two attacks that happen quickly. I also always dodge (or at least try to) their special charge move.
There are a few circumstances where if I'm taking down a small gym, level 2 or 3 I may just power through it and only dodging a few times as I try to max my damage.
Overall though I'm a dodger. It is why I have always used Jolteon for attacking Vaporeon - even before the buff - as I can get tons of attacks in between dodges. Love my Jolteons.