What problems are there for types in .aj files?

There are several known issues for types contained in .aj files.

They are not found when using code assist (Ctrl+Space).
They are not found when using add import (Ctrl+Shift+M).
They are not found when using organize imports (Ctrl+Shift+O).
There are no quick fixes available (Ctrl+1).
They are not included in Java searches.
They are not included in Call Hierarchy lists.
It is not possible to run JUnit tests written in .aj files.

AJDT intends to add support for these features in .aj files in future releases.

Creating a new aspect
Converting file extensions