PETs:  The new PET's resemble wristwatches, and instead of having a screen to view the navi, it projects it as a hologram.

Navi Customization:  Morbid as it seems, people actually go out in search of rare navi data fragments left over from the explosion to add on and upgrade their navi.  It might seem kind of creepy, but hey, it gets the job done.

Cities:  New cities have sprouted up, such as Techopolis and Dark Town, each with their own net an shops.

Navis:  Last of all are the new navis.  Aside from all the new, user made navis, there are way more story-only navis.  You can tell these navis from the others on the custom navi boards by the black color-code.

Viruses:  With viruses, it's kind of good news/bad news, depending on whether you like combat or not.  There are over thirty new viruses so far, each with their own unique battle chip.  They will be avilable for purchase if you don't feel like fighting them first.