True, using today's off-the-self software it is easier to customize your environment using full virtualization compared to containers. But it isn't an inherent limitation of the container approach. Containers do however, provide inherent cost savings compared to full virtualization.
I expect that in a short amount of time, usability for containers will continue to improve. See for example docker: http://www.docker.io/
> What if my application is built to run on Debian but yours is built to run on CentOS? With container based virtualization we have to be put on different nodes. With VMs, we can share a node.
With the cost savings afforded by containers, I expect developers will generally choose to write applications that are portable enough to work inside containers.
> This is why VMs exist. This is why they will continue to exist.
Virtualization is popular because it is a feature-rich, economical way to host. Containers are more economical and I expect will win in the end.