The difficulties you mention (aside from upgrading servers) is about the having multiple apps in a single server not standalone vs embedded. Although, if you are careful, it can actually be faster and easier to deploy to a multi-app server [0].

I grant you, upgrading servers can be more involved depending on how you do it.

[0] - http://tomcat.apache.org/tomcat-7.0-doc/deployer-howto.html#...