Some advice on travelling around Mexico

I can't figure out from your post which airports you will use to first enter Mexico (at Cancun perhaps) and later depart from the country (maybe flying out of Mexico City).

Perspective--Mexico has far more extraordinary ruins/ancient ceremonial sites, vibrant cities, and attractive natural areas,including beaches, than any traveler can experience in just two weeks. So, before selecting prospective destinations, first consider your priorities the kinds of experiences that you most wish to have. Once that is decided you may discover that some locations that are not currently on your list could be satisfactorily substituted for others, in the process reducing the amount of time and money that you'll need to devote to moving around the country.

Your profile says that your current location is London, in the UK. So, you probably booked both your arriving and departing international flights using Cancun's airport. Fares to reach Mexico from Europe and the UK tend to be cheaper done that way. If that is your plan, consider either:

A. Spending all two weeks on the Yucatan Peninsula, possibly circling it and detouring slightly into the lowlands of Chiapas State to Palenque. OR

B. Dividing your time between locations on the Yucatan Peninsula and in the Chiapas highlands, including San Cristobal de las Casas. That would be and "out and back" itinerary during which you could break up the bus journeys so that none would be longer than 8 hours. OR

C. Dividing your time between locations on the Yucatan Peninsula (especially its more accessible northern sections) and the Mexico City area. That would include flying back and forth between the Peninsula and Mexico City. The cheapest air links are likely to be between Cancun and Mexico City. But, its also possible to fly one way between other regional cities, such as Merida for example, and Mexico City.

Agree with #1, your proposed itineraries are a bit confusing.
But maybe check some Aeromar's routes, they fly between many/most of your propsed destinations without necessarily rerouting through MEX. As an example, they have Oaxaca>Tuxtla, Villahermosa>Merida.

As tempting as it may seem, I wouldn't put all your eggs in the "one flight" basket... those obscure routes are notorious for being canceled due to poor ticket sales or other circumstances.

Consider doing Mexico to Oaxaca, Oaxaca to San Cris on an overnight bus (these are luxury vehicles, it's not as bad as it seems), San Cris to Palenque, Palenque to Yucatan. It's a lot for 2 weeks, but not much worse than doing tons of back and forth flights.,

Book a flight, overnight buses suck, what do you do at 6 am when the bus arrives, nothing's open, you can't get into your hotel for 8 hours, you've not slept or bathed or brushed your teeth. Ugh. Extremely doubtful that #2 has ever even booked such a flight and had it cancelled, so he wouldn't know anyway. Besides, the odds of a flight cancellation are probably on par with your bus being blockaded in that part of Mexico. Even so, in the rare case your flight does get cancelled, #2 would be the first to tell you that you can show up at the central an hour in advance and be able to buy a ticket.

Thanks for the responses, everyone - it's all very useful to hear.

Just to add that we're flying in and out of Cancun (from the UK). We were originally looking at just the Yucatan Peninsula and taking our time about it - but there are various things in and around Mexico City, in particular that we've decided we're keen to see. Palenque/San Cristobal and Oaxaca then looked like good destinations to breaking the route up.

So if we're in and out of Cancun and do want to include Mexico City, I'm wondering if we skip Oaxaca and do:

Chichen Itza/Merida 1-2 days (8 hr overnight bus to Palenque)
Palenque - 2-3 days (risking that once-a-week direct flight to Mexico City)
Mexico City - 5 days (flight back to Cancun)
Tulum - 4 days

... and use those last few days to explore Yucatan more thoroughly.

Any thoughts on that plan?

Not to complicate things but I think it's really a shame to only spend 2 days in the Yucatan. For example, Uxmal is a far superior site to Chichen Itza and it should not be missed if interested in Maya archaeological sites. Then there are numerous cenotes and haciendas and Merida, itself, is worth at least one full day. You say you will explore the Yucatan out of Tulum but that's a whole different world than the state of the Yucatan.

You might consider skipping Merida altogether - come back another time - and go from the Cancun airport to Valladolid for two days and using that as a base for Chichen, Ek Balam, and a cenote or two. (A little research will get you away from the hyper-touristy and commercial ventures). Valladolid is a charming and attractive small city.

I like your second plan better.

Consider flying from Cancun to Mexico City (3 days) as soon as you arrive, and then; Oaxaca (3); San Cristobal de las Casas (2); Palenque (1), Merida (2); Valladolid (1); Tulum (2); Cancun. There are overnight first class buses between many of these places, if that suits you, so you don´t waste day time traveling.