We visited this yesterday, first walking to the top of the hill to visit La Iglesia de los Remedios and then making our way down to the Pyramid. It was fascinating to view 2000 years of history built and built over. Honestly when we first saw the pyramid with the church built upon it we felt it was an apt example of one culture trying to subsume another. AO and the tour soon set us straight.
The whole city of Puebla is well worth the visit to see what this crash of cultures has produced. The architecture and the equally beautiful people (not to mention the fantastic food and drink - try the insectos!) are things to see and learn from. Even though the pyramid was covered before the Spanish arrived, it is a great analogy for the arrival of Spain and the near destruction of a great civilization and the roots that still grow and nourish it.