Been to both. Chose Puerto Vallarta. Better climate in PV. PV is by the bay.. Beautiful views! PV is easier to fly from US. More expats here. Lots of art and culture here. Beautiful natural scenery. Merida is more of an inland city. Progreso it’s near beach town Seems it’s a bit run down. More buggy and muggy in Merida. Lots of history and culture here too. Has many Mayan sites nearby. A few hours drive to Cancun. Nice housing a little cheaper in Merida. Fewer expats. Not as touristed like PV. More prone to hurricanes. More of a city then PV which feels more resort like. We love living by the beach. That’s a major reason for PV.
We chose the Riviera Maya over both of these. Our main reasons for the RM over PV included 1) A love of the gorgeous Caribbean Sea vs the Pacific and beaches there. 2) so much easier to fly into from the NE US. The Mayan culture and history The close proximity to other areas like the state of Yucatan, Costa Maya, and Belize, as well as flights to other areas of the Carib. We chose the area round Playa Del Carmen over Mérida for the above reasons, plus Mérida is more a large city that can be very hot. It is a beautiful cit to visit though!
Having said all that, with your interest in mind - a small fishing village within easy reach of shopping and entertainment (as well as quality medical services) - I would suggest considering Puerto Morelos which is a short drive from Playa Del Carmen to the south, and Cancun to the north. Or to the south of Playa, Akumal or even Tulum.