I am now picturing a scenario where the Aztecs or Inca go Protestant, or even Muslim, simply to spite Spain.
Well with trade with England and the Dutch, a Protestant Aztec or Inca Empire could be possibly.
It's always possible, but given that it was the Catholic powers (Spain and France especially) who engaged in colonial proselytizing, I think it less likely and imagine some sort of syncretism will develop.
Also, if Spain doesn't have its great influx of mineral wealth, the Protestant Reformation and aftermath will play out
much differently. For one example, Charles might not have as many mercenaries, resulting in no Sack of Rome and a proper annulment for Henry VIII's first marriage, which could result in a Catholic England.