I'm also cruising Panama Canal Nov 19 but with Holland America. I thought I'd reply to you because I have spent a number of vacations in Huatulco.
Huatulco is the area. Within that are 2 towns - Bahia Santa Cruz is where the ship docks, and La Crucecitta. They are side by side and you can't tell when you're actually leaving one and entering the other. Santa Cruz is very small and not densely populated, and La Crucecitta is the bigger but still far from being a 'city'. The area includes 9 bays, some totally undeveloped as they are protected and within a national park area. Others are developed but by north american standards they are more towards primitive. Bay tours will all have a number of these and probably stopping to snorkel at one of them. In November the jungle will still be green (its quite brown and dry by January) and it will be pretty to view from the water. This shows all the bays and towns. The bay tours will encompass, for the most part, the bays from Oregano to San Agustin.
Santa Cruz is very small. You will dock at a fairly short pier in an area that has an small expanse of beach which is very nice for swimming and lined with restaurants. Behind that is a marina and some shopping. There is a nice square with a gazebo in the centre that serves great coffee in all forms (Cafe Huatulco). There will also be many taxis, all who will be willing to take you somewhere. Just a ride within the area is very cheap and I'd recommend having pesos. Taxi rates are posted and, in all my time spent vacationing there, I have never been ripped off by a taxi trying to charge more than the posted rate. Taxis are more than plentiful everywhere and always looking for a fare so if you stay within the area, you needn't worry about not getting back to the ship on time. Within this area you will always be able to see the ship in the bay. If you're there on a Saturday morning there may be an organic farmer's market in the square surrounding Cafe Huatulco.
About 40 pesos (perhaps less) will get you to La Crucecitta to 'centro'. It is also walkable although it is very hot, humid and sunny. There is a newly built walkway that leads out straight from the ship and up and over a hill. While on top of that hill you get a great view of the ship in the bay. La Crucecitta is a great area to walk around or sit in the square, have some ice cream and people watch. It's difficult to get lost and I'm sure you could download a map of the town before you go to help you along. The big Lady of Guadalupe church is right in front of the square.
The Copalita Ruins are interesting but IMO not worth the price of a ship excursion. You can easily take a taxi there, pay admission, and go on your own although guides are available for rent once you get there. We did not get a guide but then, we didn't really want all the history explained to us, we just wanted to see it all. It is quiet and jungle like with wide, flat and well defined paths. The ruins themselves are not "WOW" but they are ruins. It's a great area for bird watching, too, because it is quiet. The walk eventually takes you up to a lookout that overlooks where the Copalita River enters the ocean. That view is stunning. That beach that you overlook is called La Bocana which is my favourite place of all in Huatulco. When you exit the ruins you can go (walk or cab) to La Bocana - there is a very small village with cobblestone streets just before the beach. We like to walk the beach to the river and watch the birdlife there as there is also a lagoon that has formed in this area. There is often a crude shade structure and some driftwood to sit on. Beautiful, beautiful place. Local fishermen are sometimes there net fishing from the beach, and there will probably be a few ladies who will offer a mud bath. Maybe some surfers. If you go, and feel like a snack after that, Los Gueros in that little village has the best fries (among many other choices). The taxi driver will arrange a time to come back and get you.
Any of the ship excursions that involve country will, no doubt, involve a drive up into the mountainous area to Santa Maria Huatulco, coffee farms (Pluma Hidalgo), waterfalls (in the Magdalena River), or a botanical garden (Hagia Sofia). These drives always leave me with motion sickness and a headache because they are so twisty. Any bay tour will take in generally 3-5 bays with a stop for food and/or snorkeling. If you like snorkeling, I'd recommend simply a taxi from Santa Cruz to L'Entrega - cheap and close by and you can snorkel from the beach. Rental equipment is available there along with plenty of restaurants to sit at. The botanical garden is interesting but it is not the term I would have used as it has a more of a wild feel to it.
Culture may involve going to the town of Santa Maria Huatulco which is enroute to the mountainous area. Again, very easy to take a taxi there and back without issue. Aside from wandering around, shopping and eating, I'm not sure what the draw there is. It is the home of residents displaced by the development of the Huatulco resort area.
I hope this helps some. I'm going back there again for a couple of weeks in January - this time I'm hoping to go to the town of Pochutla on a Monday to take in the big market and to Yee Lo Bee Parque Mariposario, a butterfly sanctuary (mariposariohuatulco.com)