my wife and I are on Sapphire Princess on the October 11 sailing. We have done this itinerary many times and there will occasionally be a rough day or two; but it is really only noticeable on the smaller ships. As you point out, Sapphire is a large ship and very stable. You are usually not even aware you are on a ship.
Not knowing your interests, it's hard to suggest a "must see"; for some, a zip line is a "must do": for me, it's a "must avoid at all costs".
But we usually spend our three port days like this;
Puerto Vallarta - taxi into town; walk around, window shop, visit the church, walk down to the river and have a cold one by the beach; walk the promenade back to the center town, and taxi back to the ship.
Mazatlan - taxi into old town; walk around, visit the Cathedral. Then taxi to the Golden Zone for lunch at the Shrimp Factory and some serious shopping. Maybe a swim at El Cid.
Cabo San Lucas - best beaches and water sports. Definitely take one of the excursions that takes you by boat to Los Arcos for a close look at one of the most famouse rock formations on the West Coast.
As I said, we've been there many times so we just play it by ear--whatever we happen to feel like when we get there. But if it's your and your friends' first trip there, you might want to stick with the ship excursions. You will see more in the time you have there.
Have a great cruise. Which date are you sailing? It would be fun if we are on the same one.