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I have done a couple of large projects in agol and had some pretty serious issues.

  * Vector layers are fast but you cannot easily query attributes for a shape within the esri web apps.
  * Feature layers are dead slow for large datasets.
  * The API sometimes relies on you submitting form encoded JSON documents which may or may not actually do what you want on the backend.  
  * API error message are not always descriptive.
  * The API documentation is not great.  For example try finding the correct string formatting for a date.

It is a mass of different systems clustered together into a tightly coupled mess.