Structuring groupcontent with taxonomy I have a site with three grouptypes (organic groups).
I am still sort of finding out the right structure as i want each group type to have 
their own (predefined) taxonomyterms. (og vocab will not work as this is per group)

Should i give each grouptype a different groupcontenttype. This way i can divide my vocabularies over each groupcontentype. This way i will have a clear distinction per grouptype. However it results in more maintenance as i need to make views (filtering taxonomy) and panelpages per grouptype.

Is there some other way that i am not aware of using just one groupcontenttype for all my grouptypes and being able to set the proper vocabulary on them?
If the number of group types is relatively small and consistent, you might consider adding several taxonomy term fields to the base groupcontenttype, each referencing the relevant grouptype specific vocabulary, and then hiding the fields that are not relevant to a group's type.

If you hid the field on the node edit page using a switch statement (on group type) in hook_form_alter, then ensured that empty fields were not displayed on the node, then both visitor and admin would not see irrelevant fields.