We did the resort first and the Pelagian second. We were a group of 20 and split 10 and 10. The other group did the Pelagian first. Consensus was that getting acclimated at the resort first was a better experience. More importantly, we experienced a problem that may occur more than just to our group. The charter flight was too heavy so the resort staff took some of the luggage off the plane and took them overland. They decided to take off the plane one of each person's bag if you checked two to go under the plane. Spouse and I decided to keep our carry on bag with us (minimal clothes, regs, mask, computers, photo equipment) so they left our one checked bag each on the plane. Those who went straight onto the Pelagian and had one of the checked bags taken off the plane did not get their bag for three days. Those staying first at the resort received their second bag on day two. The resort comped everyone rental gear but many of our group were not happy and especially not happy that this was not discussed with us prior to take off. Photographers who checked both bags did not have their equipment for 2 or 3 days of diving. If they had told us before take off some would have reallocated equipment to make sure the most important was carried on the plane.
The variety of the dives on the Pelagian are slightly better than the resort dive sites (my opinion) so doing more variety second seemed better to us.
Anyway, push comes to shove, I'd do the Pelagian second.
Rob