Both the B-2 and F-22 have embedded antennas. JshWright's point seems to make sense: the complexity comes from system's integration and software, compounded by the aircraft having to be too many things to too many people.

Basically, software, of which there's a ton to say regarding F-35 development. All the features required and component integration required them to adopt an agile methodology, moving away from the Ada-style development processes and, arguably hacking things together until they kinda worked. The predictable result is a long-tail of bugs that may never be fully eradicated.