Other then one being deprecated the other being recommended, what else are you looking for?
There aren’t many functional differences, if something is deprecated, you should not use that service/library etc. It is only there for backwards compatibility, not for you to implement new services using it. It is not only meant for webMethods or SoftwareAG products, it applies to everything.
If the documentation says it is deprecated, assume it doesn’t exist.
#Integration-Server-and-ESB#webMethods