Well I can only comment on what we did across a 6 week trip:
Flew into Mex City.
In Mex city used the Metro & taxis & did a couple of day tours organised through the hotel.
Flew to Guatemala City.
Stayed in Antigua.
Did a few side trips organised through local agents (e.g. to Lake Atitlan, Chichicastenango, Day of Dead kites festival at Santiago Sacetepecuez).
Bus to Tikal.
Flight to Cancun (good transport hub, but get the hell out).
In Yucatan stayed in Playa del Carmel, Valladolid and Merida using local buses to get between.
Flight to Havana.
Stayed Havana, Trinidad, Santa Clara?, Vinales using tourist & local buses.
So yeah,bottom line - if you have the time it is easy to organise things while you are there either through local agents or using public transport. Public transport can mean anything from chicken buses to luxury coaches aimed at tourists depending on the route & the depth of your pockets.