I feel like we were able to pack a lot of things into a short time in the Yucatan, but there's so much we had to skip.
Calakmul, obviously, when we couldn't get there. There are at least a dozen other sites in the area, including some in Quintana Roo. But it's hard to get here. Not many airlines fly into Chetumal or Campeche (and it's still a long drive from Campeche) and Villahermosa and Cancun are many hours away. I'm sorry we missed our chance to go. Flying into Chetumal would be the best option for going to all those sites and Interjet at least flies there.
More sites in Tabasco and Chiapas. The only Olmec-related thing we did was the La Venta museum in Villahermosa which hardly counts, and all we did in Chiapas was Palenque (which definitely counts). There are many interesting sites in Tabasco that are best visited from Villahermosa and you could fly in and out of Tuxtla Gutierrez and do a really cool loop of Chiapas sites.
Merida. That was cut out mid-trip in favor of a few other things. I'd love to spend a few days poking around the city.