I think the last time I did that was with the 4S, maybe. It might have been even before that. It was a pain to download all the apps again and get everything set up the way I wanted. It took a long time. Since then I've always used whatever transfer process Apple had available — most recently iCloud. It works fine and I've never noticed any residual garbage clogging things up. To be honest, I remember back in the old days on Windows computers, when you bought a new computer you set it up as new and reloaded apps and such, because there was a lot of junk that never got cleared out otherwise and you didn't want that on your brand new shiny box. I think this is a holdover from that. I've never had any such issues on an iPhone.
