So got the S3 and turned it on, the apps started to install and update themselves again....but before this happened I just cut the data connection and restarted.
When you boot for the first time there's an option to backup and restore with Google, I completely forgot about this and ticked them. If you were not to tick these options on startup then I don't the phone will auto install the apps.
Haven't had too much time to mess with it as I had a 2 hour lunch, my manager also knows what I'm like when I get a new phone so she knows I'll just sit and play with it.
Edit: Was jsut about to go into GooglePlay and share an app....noticed that it's put short cuts already on my phone. Not as many as before but that's because I have disassociated my SGS 1 from Google Play.