Focus on key strengths...
The problem with the whole EE approach - in my opinion - is that Sun tried to push Java into every imaginable direction, even if that meant turning it into something it's actually not. One of the main problems which the whole approach is that the environment can be tedious in comparison to the other alternatives.
If I want to program in PHP then all I need is the Apache webserver with the PHP plugin. If I want to program in ASP.NET (my personal favorite) then all I need is either IIS ("one size fits all") or Apache with the mod_mono plugin (and Mono of course). Although this setup does use Mono as a backend (or separate application service) it's still a "one size fits all" kind of solution because I don't have to tinker with any backends, Apache is mainly calling the shots so to speak.
Java not so much. Now, I can utilize Tomcat or Glassfish for all my contents but seriously... That's not even remotely usable as a webserver, because it lacks a lot of things which you'd normally expect to find there. So you're more or less forced to using 2 environments. Your webserver and the application server backend. 2 environments to maintain, tune and optimize.
My other gripe is that a Java environment isn't really very flexible when it comes to webdesign. It heavily relies on frameworks to get the functionality onboard, but in the end it still feels somewhat of a hack to me. For example: I can't easily set it up that one webpage should be considered a master template of some sort which should always be included by everything else.
That is: you can easily include extra contents, but its always pretty static. You can work your way around all that (session beans come to mind) but if you compare that to the ease of use which both PHP and ASP.NET can provide here then Java gets a bit mediocre.
Now, that's not saying it's all bad, which is also why I mentioned key strengths. I think Java can seriously excel when it comes to building webservices. You don't have to worry about design, you don't have to worry about contents too much but mostly usability and remote access. Thats a Java concept I actually do heavily enjoy using.
And I think that might be their best bet: start by focusing on the things Java is currently good at and try to work around it.