I've really really got mixed feelings on the boxed sets... Let's divide this into pros and cons:
Pros:
Material is separated into smaller booklets--you don't HAVE to take the entire box with you if you don't want.
Maps! I loved getting several maps and having a decent place to store them.
With multiple softcover booklets in the box, I always felt like if I wanted to get a map out of one of the books for my own use, i could, because i wouldn't be hurting the book too much by photocopying it. With hardbacks, I'm always worried about the spine and all of that stuff.
You can add books/paper/notes to the box pretty easily.
The nifty little extras like cardstock sheets or a setting specific DM screen were always nice.
It does sort of feel like Christmas opening up the boxed sets...

Cons:
Boxes are fragile and easy to smash/sit on/rip etc.
Boxes are bulkier for travelling DMs
Hardbacks are much more durable.
I really don't give a rat's ass about "monstrous compendium" 5 hole punched sheets.