Enhancement recomendations:

• jUDDI is maybe a bit to singleton-centric. After the good old statement "there is nothing constant in this world", it would be good if one could run several registries (for different purposes and with different configurations) in one server, hence to shrink the singleton aspect to maybe a single class (the jUDDI service, implemented as an MBEAN)?
• Authorization data mixed with application data: Since you cannot interact with jUDDI without connecting your security principal to publisher information, setting up a fresh registry (via ddl) needs bootstrap entries. Maybe only a minor point.
• I would propose to separate the jUDDI (web) service from the transport engine (Axis servlets) a bit more (maybe by implementing their relation via a dedicated JAXRPC bean?).

Other wishes (but I do not want to sound as the usual naïve feature requestor as I know how much work are behind these bullets!):

• JAXR client implementation - administration UI (e.g., web client for browsing/interacting with a remote UDDI registry)