Calling it version 3 is a fine solution, and the spec has changed
enough from key/value 2.0 to json 2.0, and grown a year older, that
it's also appropriate to bump the version again.

appropriate to bump? "key/value 2.0" was never a thing.
I don't like switching to 3.0, unless we really have to.
It looks odd from the outside. 
like we're switching gears again in some major way

btw, what is in wheel's "2.0" METADATA file that is 2.0? and what's using it?

can't bdist_wheel at least stop setting metadata to 2.0 from here on?