In my opinion, university is really meant to teach you to be strong on the fundamentals and concepts not necessarily to teach you the exact skills you will need in a job. So most of all I would recommend that you make sure you're learning the concepts found in enterprise application requirements (e.g. transactions, messaging queues/topics, etc...) However, if this is really a concern for you I would suggest doing a self-study (possibly for course credit). Also, try to find an internship that will let you play in some Java EE code.
I was asking myself the same question when I was nearing the end of university. I'm now working in a Java EE environment and there was some learning curve to use the Java EE libraries. I have to agree with many others and say that doing enterprise java development is not very much fun compared to other projects I've worked on so you might want to keep having fun in university and put off the boring stuff for when you're part of the workforce.
