Currently the 3rd party stuff uses /_matrix/app/unstable, however by nature application services that have supported this endpoint for the last 4 years are unlikely to be happy about it becoming /v1. We should probably define that /v1 is the correct route and that homeservers fall back to /unstable if they get some sort of error code as a backwards compatibility measure.
Similarly, we should probably put /users, /rooms, and /transactions under the same namespace as 3rd party stuff, using a similar fallback mechanism.
Putting this as an r0 item to spark the discussion.