I think this trend is great! I hate to disagree, but I have so little space at home that I always threw away the bigger boxes. Back before they were book-sized they were, indeed, impossible to manage, so I always had to find space for both the manual and the CD case.
Then came the smaller book-sized ones. Though still cardboard boxes, they weren't as impractical to fit into a shelf as trophies. As the boxes (I'm not sure if they've all undergone this change) turned into DVD containers, still book-sized, it was considerably more incentive to keep everything and display; besides, here was a home not only for the CD but also the manual. A change to DVD cases was even better - less space taken up.
Now, only recently, my brother and I got RA3 premier, and, as the OP said, it's pretty small. But it's metal, contains a fair bit of paper and three CDs. Not a cubic centimetre of space is wasted => pretty much perfect economy of space.
Besides which, the psychological impact of buying a huge box and finding a single CD and a small, thin manual inside is pretty damaging. "For all this space," you'd think, "they'd at least try to justify it." That's how I used to feel; cheated of the amount of space I bought, if only subconciously.
Indeed, the largest box I bought in the last year was the WiC collector's edition, which is about the size of a really heavy-duty Raymond E. Feist novel. And, man, THAT was justified. The original CD, a "recruit your friends" CD, a "making of" CD, a Modern Marvels CD about the Berlin Wall (one where, for some reason, the German interviewees spoke at exactly the same volume as the interpreters, so it became a rather interesting challenge to make any sense from them), an actual piece of the Berlin Wall, along with a cute little certificate, and, of course, the manual. On top of all this, the box is made out of some sort of really heavy card, and covered in fabric. I mean, I got what I paid for, there. That box is pretty much packed.
In fact, had the box been bigger, I might have again felt, though perhaps to a lesser degree, that feeling of being cheated for my space. I'm happy that they keep the boxes as small as they can be. It saves space, and the space it does take up is utilized so much more efficiently that I feel, paradoxically, as if I've got more for my money.
Apologies for the rant