this is the existential question facing app engine's glacier-under-the-surface installed base of python 2 apps. the writing seems to be on the wall for the legacy, custom app engine python APIs; all signs point to the decoupled, REST-based APIs to standalone services (datastore, cloud tasks, etc) as the future.
you're right, though, we still haven't heard a migration path for long time users like us with existing python codebases that use the old APIs. word on the street seems to be that google knows this, and has been thinking about an answer for a while. one obvious reason is that there are plenty of big whale app engine customers in the same boat as us (
ahem) who presumably have more leverage.
i have no inside knowledge, but my bet is that we'll get some form of compatibility layer, either porting (most) old libraries to use the new REST APIs under the hood, and/or (less likely) a code transformation tool like python's 2to3. i doubt either one would handle 100% of existing code, but if they hit 80% or 90%, i expect they'd declare victory. here's hoping!