I work part time at Gamestop, and I have seen new 3DS & Xbox 360 games with "heat sealed" wrapping as well as with the "Y" fold wrapping. I see the heat sealed wrapping more and more lately.
Each uses a slightly different type of cellophane as well. The Y fold cellophane is very crinkly, while the heat sealed plastic is more like Saran wrap.
The games that I've noticed this on are brand new releases, so it's not like they are older "gutted" games that have been re-wrapped and sent to us.