Hey Denis,
You're right in that there's no special plugin feature that allows you to configure a constructor's prototype directly. Aside from creating a new plugin (I saw your gist, but haven't looked at it closely yet), another option may be to use `create` to create an instance, which you can use as a prototype for creating other instances.
I've used that in several situations, and it has worked out well. It's very much like using Object.create.
Rather than using wire to do it, another option might be simply to create a module that begets a new constructor+proto from the original using Object.create and configures it. Then you could `create` instances of that new constructor using wire. That spreads your configuration out a bit more, so it may not be ideal, but again, may be fine depending on the situation.
If you do go the route of setting properties on an existing prototype directly, just remember that you'll be modifying the prototype for all code in the same VM that uses that prototype. Personally, I'd probably look for another way, but as long as that's ok for your situation, creating a plugin to do it would probably work out well.
Cheers,
b