Before an extreme drought hit them, they had large cities, communal infrastructure projects (mainly water storage and tempels), lots of knowledge, and so on.
In a report I once saw on tv, natural weather patterns, completely independent of local agricultural methods, were made responsible for the drought. Apparently, every few hundred years, freak weather patterns can cause the tropical Yucatan peninsula to hardly get any rain for several years.
To avoid a PoD which includes climate changes, the Mayas would need to be sufficiently developed to be able to solve their water problems, or there would need to be something which enables them to recover quickly after such a drough.
As it was, the drought apparently caused a civil war, which destroyed the Maya civilisation even more than the lack of water. When the Europeans arrived, the Mayas still hadn't recovered, and the few remains were decimated again by old world diseases.
The simplest change might be a society more able to adapt to hardships. As it was, a class society where people showed their position by "improving" their looks (dental changes, among others) delivered perfect targets for mobs and war lords. Thus, the elite was killed and with it lots of knowledge and organisation. Both a more egalitarian and a more suppressive society might have been able to avoid those problems, which would have led to a fast recovery of the population numbers once the rain sets in again.
But for the Mayas to be able to stand up to the Spanish, they'd need earlier contact with Europe or Asia - both for disease resistance, as for technology. Maybe if their society hadn't imploded, some merchants would have discovered first all the riches available in the Americas (plants, agricultural methods, ...) and then the currents and winds enabling fast passage to Africa or Europe and back.
