When we were tossing this idea around earlier it was decided that pyramids could probably become the facades of new mosques but now I'm not so sure. The symbolism in the architecture of a pyramid and a mosque are totally different-- each level of the pyramid, the ascent from bottom to top, and even sending a dead body rolling down the stairs are all what pyramids were built to represent. Meanwhile I feel like mosques are supposed to be as flat as possible-- no one is
ascending or
descending anywhere, at least not yet. You could keep the pyramid and then just build an enclosed space around it, but 1) "big pre-Islamic structure in the middle of a Grand Mosque" sounds way too much like the Kaaba and 2) Mesoamerican pyramids are really big, plenty of them are bigger than the Egyptian pyramids (and some are built to be wider than a regular pyramid, making them even harder to enclose). You could simply make the roofs of an otherwise normal building more pyramid-esque but that's more cosmetics than anything. I suppose you could also slice a few layers off the top and use the remainder as a raised platform to build a mosque on but that's about as "native" as the
Qorikancha. Still could lead to a cool contrast effect though, between the foundation and the structure on top.