Specifically you don't need to create a schema, xml mapping and POJO model. In most cases you ONLY need the POJO model. The XML mapping is almost never needed and the schema (DB structure) is generated automatically from this POJO model. Hibernate specific config is certainly not the norm to have, especially not in its own file. At most you may want to set one or two attributes in the Java EE/JPA standard persistence.xml file.
You also rarely need any GlassFish specific config. It exists, but needing it is the exception rather than the rule.
I wonder how you can talk about both hibernate and GlassFish configs btw. GlassFish ships with EclipseLink, so you don't need hibernate as well (they both implement JPA and will even conflict when used together).
I think you're indeed mistaken ;) Java EE had a bad reputation in 2004, being mainly represented by mega corps with their hidden corporate agendas (IBM, BEA, Oracle). Developers weren't being asked what the wanted or needed managers were influenced by sales teams to go with either IBM or BEA. Application servers were at least a 2GB download and easily required a GB of memory to run (this is still a lot in 2014, go figure what this was in 2004). Of course everything was closed source, super expensive (so your company never updated) and servers took a minimum of 5 minutes to boot up. A hello world in the then dominant EJB 2 technology required implementing 3 interfaces, inheriting from a base class, using a special compiler tool to enhance the class another compiler tool to create stubs and needed some 20 lines of XML in an incredibly verbose format to be registered.
You didn't need to be a technology export to predict developers didn't really like this tech (understatement of the year).
In 2005 Sun made a dramatic turn, and Java EE 5 started focussing on developer demands instead. Meanwhile many open source initiatives started or were getting mature (Sun's GlassFish, JBoss, Apache's Geronimo and recently TomEE).
Java EE 6 (2009) and EE 7 (2013) continued this trend.
Long story short, completely free and open source servers that start in a second or less and are between 30 and 120MB to download now dominate the market. The APIs have been dramatically simplified and the process of contributing to the platform has been largely opened, making it possible for anyone to create issues, submit patches or discuss the future direction. There's one thorny exception and that's the so-called TCK: a test suite that checks spec compliance is still mostly closed.
And yes, there are now hip startups using Java EE, for example http://zeef.com
All in all Java EE has become somewhat of a secret weapon. It's powerful, yet lightweight and quite a lot of people have not (re-)discovered it yet. Especially when combined with Java 8 (due for release next week) it's a very good stack.
