I am planning to migrate some applications currently running on tomcat to spring-boot running tomcat embedded.
The current setup is that each app has its own instance and they don't share any common resources.
What are the current limitations on using the embedded tomcat?
Well, the limitations are a mere consequence of the feature itself. Since it's not a "container", you obviously can't deploy multiple webapps in the same process, and thus can't share managed resources (like connection pools) between them, and somewhat duplicate the need for server configuration (but in a sane environment, everything can be automated).
Also, from the docs, there are some limitations related to JSPs.
Other than that, you're running a vanilla feature-complete tomcat, so there shouldn't be any problem.