I spent three weeks on the Yucatan peninsula and one week in Costa Rica and while in Mexico I felt like I had enough time to see a lot and enjoy the trip, Costa Rica felt too short. I spent half the week on each coast, and I should have picked just one, and stayed longer if I wanted to see everything, since I missed some areas that I was really interested in. If you only have 1-2 weeks, I'd say pick one place, if you want to do both, try for a month. But also, I hope you mean after covid, please don't travel during a pandemic.
I'm not an all inclusive resort person either, I booked airbnbs and rented a car in Costa Rica and took public transit in Mexico. Plan for driving to take a bit longer than you expect due to the road and traffic conditions.
One thing, San Jose is not necessarily a great retirement destination, depending on what your dad is looking for. Admittedly I didn't spend much time there but the real beauty of Costa Rica is the nature and animals, SJ was busy and crowded and a nightmare to drive in.