We chose a combination of Mongo/Dynamo for a healthcare product. Basically mongo allows better searching, but the hosted Dynamo is great because its HIPAA compliant without any extra work. So we host the mongo portion with no personal data on a standard setup and allow amazon to deal with the HIPAA portion in terms of infrastructure. We can query certain items from mongo which bring up documents with pointers (ID's) of the relatable Dynamo document.
The main reason we chose to do this using mongo instead of hosting the entire application on dynamo was for 2 reasons. First, we needed to preform location based searches which mongo is great at and at the time, Dynamo was not, but they do have an option now.
Secondly was that some documents were unstructured and we did not know ahead of time what the data would be, so for example lets say user a inputs a document in the "form" collection like this: {"username": "user1", "email": "me@me.com"}. And another user puts this in the same collection {"phone": "813-555-3333", "location": [28.1234,-83.2342]}. With mongo we can search any of these dynamic and unknown fields at any time, with Dynamo, you could do this but would have to make a index every time a new field was added that you wanted searchable. So if you have never had a phone field in your Dynamo document before and then all of the sudden, some one adds it, its completely unsearchable.
Now this brings up another point in which you have mentioned. Sometimes choosing the right solution for the job does not always mean choosing the best product for the job. For example you may have a client who needs and will use the system you created for 10+ years. Going with a SaaS/IaaS solution that is good enough to get the job done may be a better option as you can rely on amazon to have up-kept and maintained their systems over the long haul.