For the Analytics 2.0 APIs, the throttle limit is set at 120 calls per minute, per user, regardless of report suite or company. When the throttle limit is crossed, the server returns an HTTP 429 status to the user the with message content: "too many requests". Note that the throttle applies at the API gateway layer. The throttle limits can't currently be raised.
There is also a throttle applied by the underlying reporting engine per report suite which is independent of any reporting client (e.g. Workspace, Report Builder, API, etc.) When that throttle is hit, no errors are returned but report requests take longer to process. The end result is that report requests across all clients take longer to process as the load on the report suite increases. Thus, it's possible for Workspace or Report Builder usage to cause API requests to run slower and it's possible for API requests to cause Workspace or Report Builder to run slower on a given report suite. The Analytics reporting system is a shared, multi-tenant system and this throttle is designed to prevent reporting activities on any single report suite from consuming too high a percentage of the capacity of a given data center.
With a throttle of 120 calls per user per minute it will indeed take more than 20 minutes to complete the thousands of breakdown calls you're making. Previous versions of the API made the multiple breakdown calls for on behalf of the caller; however, this has the effect of "hiding" the performance costs of large complex breakdowns to the callers. API calls in the previous version were queued and processed because of the load they placed on the reporting system. Callers had no idea how long a breakdown call would take and couldn't display any sort of progress while a large breakdown request was working its way through the queue.
API 2.0 doesn't do any queuing at the API layer but it requires callers to make the breakdown calls themselves. Callers can know exactly how many calls need to be made and thus calculate and provide an indication or update on progress when working through large multi-level breakdowns.
Note that API 2.0 is a reporting API designed to support responsive interactive reporting and exploration but is not well-suited for bulk data export use cases. The 1.4 Data Warehouse API or Data Feeds are more suitable for use cases that require bulk data export. You might want to investigate an hourly data feed for your use case.