I'll prefix this with "I'm not a language design or modularity design expert". I personally would have preferred that JPMS was treated as an internal JVM/API concern. This still would have meant changes for IDE and tools vendors (rt.jar going away required rework for sure) but would have given more flexible options for a user space modular system to be build on top.

An example is that the Module definition file (Module-info.java) is in Java source code. Despite the compile time benefits (performance, security etc) this brings, it really locks down how user level module systems need to interact with this. I personally would have gone for a straight XML/JSON/Manifest.MF/YAML/Whatever format which wasn't tied to the Java compiler so tightly.