Probably the mess of icons on the homescreen with text (especially all the useless Apple crap), and a convoluted settings page. When you compare it to Android's where you can have a simple look with clean round icons placed wherever you want. As iPhones are getting bigger, having more and more rows and columns of giant icons make it look messy.
Oh that. Definitely a lot of extra Apple crap which just gets organized into an unused folder...do it once and you never have to do it again.
As far as putting icons where you want, I found that to be a nice feature on tablets, not so much with phones...shrug.