mrsdoctau and I on our last few days of four months in Central America, and spent a month in Mexico at the start. It's a different kind of trip, "screw jobs, lets go backpacking" rather than a family adventure, but hopefully some info may help.
Some parts of Mexico can be dangerous, but that's true everywhere, and if you're avoiding the "reconsider" areas and the border with the US, then it shouldn't be any different than most of the world. Take the usual precautions, watch out of the usual scams, etc. We heard from a number of people that you can encounter problems while driving, police wanting bribes, sometimes carjackings and so on, but no-one we encountered personally knew anyone who that had happened to - it was all friend of a friend stuff. I'm sure it does happen occasionally though.
The furthest north we were was Mexico City (aka District Federal/DF), where we flew in, so I can't offer any advice on the first part of your trip. Mexico City is a huge city, and surprisingly we like it. We don't normally find cities that large too enjoyable, but at least in the parts we were in, it was nice. We stayed in the Roma colonia, which has lots of nice restaurants and several craft beer places. Chapultepec forest and castle is near there, and quite interesting if you like that sort of thing.
Teotihuacan is definitely worth visiting. We went on a tour which included a trip to an obsidian workshop, who also sold mezcal produced nearby, and they were very generous with the tastings, so we were a bit tipsy climbing the pyramids. You haven't been allowed to climb one of the big two for a while, and our guide said that they were stopping people climbing the large one in March due to it being vandalised too much
The different regions of Mexico have different cultures and foods, and one thing we were told to try was "tacos al pastor", which uses shaved meat like schwarma or a diner kebab. El Huequito is a chain that does it quite well, but there are a million places which serve it, including many street stalls.
We skipped Puebla due to timing, but I've heard it's worth a visit.
We were in Oaxaca just before day of the dead, and unfortunately not there for it. Oaxaca is the home of the seven moles, so definitely try some of those while you are here. The Monte Alban ruins are near here, much smaller and less touristy than others. I like ruins so went, but not high on the list of ones to visit so can easily be cut from the list if you don't want to see them all. We did a cooking class in Oaxaca (
La Cocina Oaxaqueña | Cooking Classes in Oaxaca, Mexico.) which was excellent. We spent time at the market in the morning, then a few hours cooking and eating.
We went to San Cristobal de las Casas (where we spent day of the dead) and Palenque. Some of the more indigenous towns near San Cristobal are quite interesting. The Palenque ruins are still half overrun by jungle, although a bit ruined by the people selling things, including those really annoying devices that make a sound kind of like a howler monkey. There isn't much else to do in Palenque. Oaxaca to Merida is a long trip if you don't have much to see on the way, so flying is probably a good plan.
Although there wasn't that much we did in Merida itself, it was very friendly and pleasant. We suffered due to the heat and humidity, with the average night being around 24 and day 35, and no air con in our room. Unfortunately we skipped Uxmal, which I have heard is a good set of ruins. Chichen Itza is definitely worth seeing, but overrun by tourists and hence the number of people lining the paths trying to sell you cough. There is a light show at night you can see (it costs extra), but it doesn't run on Mondays so we didn't get to see that.
We did a very long day trip from Mexico with a small group, going to two cenotes, Chichen Itza, and a brief stop at night in Valladolid. Valladolid looked quite nice, but needing to get to our flight to Cuba, we didn't return to visit during the day.
The ruins at Tulum aren't the best set of ruins, but being on the cliff tops makes them quite cool. The ones at Coba are scattered amongst trees, spread out quite a bit although you can hire bicycles or go on a bike taxi. The main pyramid is quite tall, you pass the tree line half way up. The view from the top, with the Yucatan forests stretching into the distance, but could be a difficult climb if you have problems that make that kind of thing hard. Definitely go see several centotes while you are on the Yucatan peninsula. There are thousands of them, so you'll have plenty to choose from. Dos Ojos is amazing, but I don't think you can get into the second eye unless you have at least an Open Water diving cert. The beaches along the whole Caribbean coast are amazing, we spent a lot of our time on those.
The Iguazu falls are amazing, but a long way out of the way from Mexico unless you're heading south anyway. If you do go there, I would recommend seeing both sides, and doing the Brazilian one first if you can. From the Brazilian side you get to see the wide overview, and from the Argentinean side the close up. As the locals say, "The Brazilians have the views, the Argetineans have the waterfalls".
Cuba was a very interesting place, both good and bad, but five nights may not be enough unless you are just quickly seeing the sights or staying on a beach and not experiencing much of what Cuba is. You could have two nights in Havana, go to somewhere not too far away for two nights, and then back to Havana or onward to somewhere like Varadero for a night, if you wanted to quickly see some places.
If you're heading further south along the coast, Belize is an option. More expensive than most of Central America, but that's probably less of an issue as it was for us. You could head out one of the Caye for a few days, and the snorkelling is amazing, but if you don't want much more beach time then it may not be worth it. We didn't spend much time on mainland Belize apart from San Ignacio near the border with Guatemala.
Going to Flores in Guatemala and the Tikal ruins may be another option, but it may take more time travelling overland than you are willing to spend with the limited remaining days at the end.
