They will be, just not everywhere. I'm sure they'll be there for things like battling and Super Training, where it seems to be "made" for 3D. And my guess would be that some of the more elaborate locations will be 3D as well, whereas the "limited" parts might be for things that don't really need it, like PC storage.
I don't know that many people even use the 3D. Personally, I like to look at it quickly every now and again, but predominantly it's off, so this isn't too disappointing. I'm sure future installments will make better use of 3D, if GF wants them to
I never turn 3D off, it's always turned all the way up for maximum immersion. Regular DS games not withstanding.
If this game really does limit the 3D, I'm actually really disappointed. Man, tough month for 3D. First The Little Mermaid 3D barely gets advertised (not to mention no lenticular slipcover and a glaring error during "Part of Your World") and now Pokemon 3DS isn't really in 3D? Lame.
Masuda and me: http://imageshack.us/a/img89/3412/bnax.jpg