If you get rerouted due to weather or mechanical, you might get booked into the Y fare bucket, giving you a 50% bonus for EQMs. So if that happens, you might be able to get enough miles even if you don't take all of the flights on your itinerary. There's always the possibility of calling and requesting mileage credit for your original itinerary although there are varying accounts of success using this approach.
A few years ago on my first MR, I made it to the east coast where I encountered a mechanical issue that jeopardized my getting home - the GA in PHL looked at my crazy itinerary (SMF-SFO-SAN-PHL-IAD-IAH-DEN-SFO-SMF) and sent me back home PHL-IAD-ORD-SMF in Y bucket, so I got home sooner with more EQMs.