I can't speak to Galapagos diving as unfortunately, I've not been.
However, I've been to Machu Picchu. To me, it's a must do trip. We flew into Lima late at night and stsyed at a hotel directly across from the airport, returned to airport in the morning for our flight to Cuzco. We stayed in Cuzco for a couple of days to acclimatize and were able to store our larger suitcases at the hotel while we went on to Machu Picchu by train. The train ride was enjoyable, just make sure you're not on the backpacker train, which you may not enjoy as much. We then stayed in town (Aquas Calientes sometimes called Machu Picchu Pueblo). We took the bus up the winding road to the site. The first day, we took a guided tour but the second day we showed ourselves around. I thought it an amazing place and would love to go back. I regretted that we didn't stay a bit longer but my friend thought two days was the right amount of time.
We returned to our hotel in Cuzco, retrieved our luggage, stayed the night and the next morning flew back to Lima to continue our time in Peru.
If you have the time and resources, I urge you to go. And if you've even more time and resources, go to Argentina too, which has a tremendous amount to offer. That said, I'm encouraging you to go there especially to visit the Iguazu Falls. Spectacular, but again we only gave it two days whereas I'd have happily stayed another day or two.