Hi Jens,
I deployed three private instances of Wikibase, one of which I use personally to collect some structured notes.
I've found some Wikidata configurations/customization in the code that are not useful in a wild :-) installation. Also is a bit limiting using only Commons for media, because maybe I need to use local mediawiki images.
But the greatest lack I perceived is the impossibility to use Wikidata items. For example if I want to extend a concept already described in Wikidata, for the moment, I must recreate everything in my local wikibase instance. Instead I wish I could be able to leverage more the linked data. That's my dream!
In general the guide is quite clear, also for enabling RDF API (with EasyRDF). I've just got some little problem with versions conflicts.