The only disadvantage I found with prepaying was that I could not prepay for the "preferred lot" or whatever it was called and also could not upgrade to that lot when I got there. It was nice to be able to just scan the bar code on my phone and to have that part of the trip already paid, but I would have liked to have used the other lot, given all the factors of our family.
Similarly, I wish I had gotten the sun pass or whatever the prepaid tolls thing was - probably would have saved us about thirty minutes on the drive from Orlando to the port.