I would not remove it from certain profiles, even a "Custom profile" if you look at "MicroProfile" there are so many different subprojects, features and technologies and several are barely used by a single vendor while others have much broader support. In that sense given some large companies use SOAP in very long term projects (some won't even go in production before ~2 years from now, but then have the potential to run for a few decades) I would not completely remove or expel it.
There are so many competing Web UI frameworks that e.g. adding MVC beside JSF, JSP and who knows how many others makes almost no sense either.
In particular profiles like one that depends on REST MVC sounds like a good match since it also depends on JAX-RS, maybe unless certain standards and ingredients were better optional it could be worth the Full profile but even in the current Web Profile it seems an overkill next to all the others.
I like Reza's suggestions, although maybe "core" could rather contain something like CDI only (even smaller than MicroProfile 1.0 ;-) and there should be two pillars one for a stack based on Servlets (JSP, JSF, etc.) the other based on JAX-RS where MVC might also come handy. A "Web" stack may be a superset of these two.
Regards,
Werner