3.5" have a more durable design - the hard plastic, the spring loaded shield and, most importantly, the center disk that rested on the enclosure housing that prevented the magnetic medium from sagging.

When 5.25" disks are stored on end, they sag over time causing them to physically be unreadable. You have to store them flat. 3.5" are (mostly) resistant to this sag and therefore will be more likely to survive long term.