Current State:

With the current Directory API v2 there are only two approaches that can be taken to retrieve the complete list of group memberships of an organization. 

Approach 1 (Atlassian-recommended):
1. GET /directories/{directory_id}/users?includeResourcesCount=false
2. For each user, GET /directories/{directory_id}/groups?accountIds=[userAccountId]

Approach 2 (our alternative):
1. GET /directories/{directory_id}/users?includeResourcesCount=false
2. GET /directories/{directory_id}/groups?includeResourcesCount=false
3. For each group, GET /directories/{directory_id}/users?groupIds=[groupId]&includeResourcesCount=false

Results:
includeResourcesCount=false resolved timeouts on the users endpoint.

We can now paginate all users at limit=100 in ~34 minutes.

Neither group membership strategy is viable at a large scale:

Example:
v1 (expand=GROUPS): ~15 min, ~2,000 calls (production baseline)
v2 per-user group lookup: ~13+ hours, ~98K+ calls (120 req/min limit, 97,964 users)
v2 per-group member lookup: ~22+ hours, ~10K+ calls (50 req/min limit, 8,815 groups)

Proposed Future State:

Efficient group membership retrieval in Directory API v2, similar to (v1 expand=GROUPS equivalent needed for migration).

Alternative (e.g. Third Party Plugin):

None