Also obsolete is the layout style “Old style layout with no left menu”. You can get rid of a lot of cruft by taking that out, and it will simplify the frames logic as well.
You might also be able to get rid of the radio button style layout. I would be surprised if anyone uses it any more.
Having header (and in fact footer as well) hook makes localizations less intrusive. Ideally a default header would bring in theme css and footer will bring in standard js. That makes it easier to propagate global changes e.g. jQuery version switch - not every script needs to be touched to upgrade core components.