We followed this itinerary from G adventures, spending only half the price including food and day tours (as opposed to G). Much as I enjoyed my G trip to Peru in 2013, I think the best way to explore is on your own if you have enough time to research and plan. There also would be opportunities to extend your trip in another direction ( eg. to the coast of Oaxaca), or to stay in another city of choice (eg. Tulum or any of the carribean coast towns). Travelling DIY also forces you to learn the language faster, and brings you closer to the locals.
We took precautions in Mexico due to preconceived ideas from narco movies, but throughout the tourist routes there were an overwhelming number of policemen who combed through intercity buses and popular streets.
Intercity travel was straightforward and comfortable with ADO bus services. Purchasing tickets early occasionally results in discounts, and they are usually reliable and punctual.
Street food was delicious and despite visiting reputable restaurants for dishes, we would prefer tacos/huaraches any time. The variety of meat means you are spoilt for choice, and every taco stand is appealing. Take precautions and only go to the stalls that look clean, and avoid those in Merida by the roadside due to the number of big buses that roll up dust and exhaust.
Overall one of the cheapest countries we visited (not including Cancun/Palenque), and an easy trip by overland bus routes.