Offer the user a default base selection with check boxes to select/deselect the various options. Options load/unload dependencies, e.g. other templates, Scribunto modules, Lua modules, JavaScript, CSS, etc.
Imported into target wiki via XML.
This is a huge task on its own so don't start including every other piece of global bits and pieces as well.
How to prevent overwriting templates and styles the wiki may already have in place?