Actually, that's where the cost savings and earth-friendliness gets better. The cases could be clear so that one side of the insert has the cover art and the back side (inside) has some simple instructions in inserting the disc and basic health/safety warnings.
When you insert the disc into the system and start it up for the first time, you'll get a message (similar to one about creating a save file saying "Would you like to view the manual for this game?" - you can then read it or not, via the system. If you opt not to read it (or when you're done reading it) you'll get a message like "You can check the manual at any time by pressing the "Home" button and selecting "Operations Manual". After you make your selection, the disc will create a bit in the save file telling the system not to prompt you for the manual again.
So, now, we've just eliminated manuals - so there goes a ton of paper and printing and cuts down on the shipping weight even further.
If necessary (for whatever reason) a small four page (one sheet, folded in half) or eight-page (two sheets, folded in half, stapled together) would fit inside the cases I linked to earlier.
Worst-case, you could still use cases of standard thickness and have DS-sized manuals/inserts. It'd still cut down on plastic, weight and size. (Again, these "eco" cases do nothing in regards to size)...