Hey there!
I am writing my master thesis, an identification key for trees. A preview is currently here: http://ec2-54-234-76-44.compute-1.amazonaws.com/ (address may/will change).
The key (filter.php) can already be edited (editor.php), but without history etc. Wikibase suits the requirements perfectly – you wrote it just in time. Characters of trees are language independant, descriptions are not; exactly what Wikibase does.
There is one point I need help with: I need a list of all Questions/Characters/Taxa, i.e. pretty much a table dump, for the editor (processing is all done with JavaScript). What way would you suggest? \Wikibase\Store only returns Entities for known IDs, and I have found no other function so far.
To distinguish between the different kinds of object (question, character, etc.) I plan to use instance-of properties and make the IDs of the used properties (instance-of, parent, …) and items (question, character, taxon, …) configurable in the extension.
Greetings from Switzerland, Simon