If by the same problem you mean that you have to understand a library in order to use it properly, I guess so, but I don't see how that's unique to Java.

I don't see any difference between having to understand annotations and having to understand libstdc++ for example, or having to learn about any particular ruby gem or node package.

Every language has to deal with configuration files. Complaining because a bunch of Java developers used XML in their projects seems trite.

I think XML actually has a lot of strengths (having well-defined-types and structure for one). If the complaint is that it's worse than JSON, well...I've seen way worse than XML (ASN.1 for instance), so idk...