I'll argue for keeping some sort of catalog as a guide to setting up future additions by the user. Maybe a new default catalog (one with high utility, like for products) would be a better first choice, then delete the lame ones.
Here is a suggestion on improving the current catalog, for product display. Please see the attachment; 'Product Display Needs Short Description'.

Moved menu links for modifications/projects/hosted-sites to only the collaboration zone.

Maybe they will get removed in a future release, but I think this is a good compromise for now -- it bolsters the purpose of the collaboration zone, yet people are also encouraged to easily nuke all of this during the Setup Wizard if they wish to.

Now the default (pre-Setup-Wizard) main website navigation is cleaner.

I am happy with how this is now. The Setup Wizard will remove the catalogues by default, but they are useful in the collaboration zone, and useful as examples.