Ease of use in terms of deployment, give simple interface to do simple stuff like Tomcat, JBoss or GlassFish.
Takes long time to start the server.
The Liferay wars need to be decorated and then deployed. Perhaps we could simplify that.
Some of the concepts are good for complexity that WAS can handle but could be simplified and better documented, like concepts of well and profile, context, etc.
A Liferay war file created using Liferay Developer studio runs fine in Tomcat, however that may not run in WAS 7.x because it needs to be decorated. I had one war for a Liferay portlet with a simple cron job, and had hard time running to WAS server. It was running on the latest free download done on my friends m/c. Other times I have seen that there are issues running a war file that runs on Tomcat but runs on WAS after lot of customization for WAS.
The corporations like this however, the product may need better vibrant community of users where issues can be discussed.