It seems a bit weird to me. I assume that Mario, his partner, and all of the NPC's and enemies would "pop out." On one hand that seems rather distracting, and on another it seems somewhat cool. Ultimately I believe that it'll be more distracting than interesting, since your eyes will be averted towards the characters when your trying to do something in the overworld (like look for a hidden item).
"They're NOT DOLLS. They're ACTION FIGURES. WITH REAL FIRE-PUNCHING ACTION." ~Francis. Super Paper Mario.~