I am trying to perform some data processing in a GAE application over data that is stored in the Datastore. The bottleneck point is the throughput in which the query returns ent
Your comment about "no need to scan all entities" triggers the thought that custom indexes could help your queries. That may entail schema changes to store the data in a less normal form.
Design a solution from the output perspective - what the simplest query is that produces the required results, then what the entity structure is to support such a query, then what work is needed to create and maintain such an entity structure from the current data.