Limitations:
- When you take the ESB, as you might have seen it exposes ports 8280/8243 (HTTP/HTTPS) in addition to 9763/9443 which is exposed through the servlet transport. In the case of ESB you need (and want) to use port 8280/8243 when you're interacting with the ESB because those are the two non-blocking high performant transports. When you deploy ESB on top of another web container, you're limited by the servlet transports provided by the container. So we can't get the desired performance out of the ESB for proxying and other scenarios.
- Complexities involving using web container functionalities. Carbon has its own clustering/caching/security etc... infrastructure. When you deploy Carbon as a webapp then we should look at supporting all those functions provided by the container for different containers. Which is complex, not consistent and in some cases sub-optimal
IMHO those were the two most important factors why it's discouraged to deploy Carbon on top of other containers. Going with a standalone deployment approach it has contributed immensely to not include web container specific "hacks" into the platform to get things done and have a much cleaner consistent platform.