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Certainly if the left and right adjoints are polynomial, then the induced monad will be polynomial, and this would seem the natural condition to impose. One would hope that the Kleisli and Eilenberg–Moore adjunction for a polynomial monad to comprise polynomial functors, though I'm not sure whether or not this is true.
Thanks, this is an interesting example. Given that neither horizontal nor vertical profunctors are primary, it seems plausible that the right kind of structure to consider here is a "double equipment" (by which I don't mean the usual "double category with companions and conjoints" perspective of an equipment, but rather an identity-on-objects double functor between double categories with some appropriate structure).
Upvoted as this does provide an example of distinct equipment structures that one might care about, but it's not quite what I'm looking for, as in these cases there still appears to be a "canonical" equipment, from which the others are induced.
@user984603: since you were asking questions about (pseudo)adjunctions between bicategories, I had expected you were familiar with 2-categorical terminology. Even if not, if you just ignore the prefix "pseudo" in the introduction, most of the words are standard category theory terms. But if you're satisfied with Cisinksi's comment, then it doesn't matter :) (It follows from Example 3.9 of that paper.)