I don't quite get the criticism against annotations. Metaprogramming and code as data seem to get a lot of love in the context of lisp, python or ruby, but a lot of hate when it happens to be done in Java. I absolutely love the powers that reflection, annotations etc give me.
The difficulty of analyzing dependency injection and "magic happens here" is overstated. Just run the code in the debugger. And if you are having problems with the auto-configuration stuff, you can always selectively disable it and explicitly define the beans you need.