As far as I understood CQEngine, it is a highly optimized Collection with an own query language and some persistence support.
Microstream is a storage engine designed to persist complex Java Object-Graphs, querying in memory data is not a concern of Microstream. Those Object-Graphs can be nearly any Object structure, from simple data objects to a complete Data Model(s). They are not limited to special data types, structures, or relations. Circular references are also allowed. The storage engine operates on native Java Objects and does not require any ORM Mapping to be performed.
Some other features are:
Loading (parts) of an object graph on demand (Lazy loading)
Type updates (class changes) with existing storages
Microstream also allows to customize the storage handling for individual types