If you are talking about how they show up under the "all" category in my apps, it has been that way for quite a while. It was a change made to the play store a while back. Probably a year ago or so. If it still shows all your apps as actually installed after a reset, the reset didn't work right.
Actually jt2000 is correct I did a reset on my brothes phone trying to get JB update and all his downloaded apps were still there I thought something was wrong as well but I did it again and did the same thing and also galaxy nexus still had me on my gmail account I believe u need to remove or gmail account b4 u reset or gal nexus to delete all our apps. Not that I'm gonna do it. Just a pain in @s
i personally like that it does that its a pain goin through all the apps youve downloaded ever to find the ones you had before
Kind of defeats the purpose of a factory reset. Especially if it leaves data intact as well which it sounds like it does if your Google account is still set up after a reset.. Now if there is a bad app or corrupt data there isn't a simple way to reset everything.
Also the fastest way to restore apps is to log on to play.Google.com from a PC and send the apps to your phone from there. I reinstalled over 50 apps in just a few minutes. It is much easier than doing it from your phone.
So how do you get into Google Now? I finally got JB last night but have not been able to really explore it yet. I remember seeing an option when it rebooted it gave me phone, google, and home or something like that. But now when I reboot it never gives me that same option again.