Dear Matt
QT has no logical coherence issues, but only interpretation problems, which are matter of personal opinion, and do not affect the logical foundation of the theory.
On the other hand, the relativity principle has a huge inherent logical problem, which is the simple fact that the most basic notion, i.e. the inertial frame, is not operationally defined, but is theory dependent, and, even worst, it depends on external theories. In order to know what are apparent forces you need to know which are the "real" ones, and, for that, you need to rely on an external theory. Unfortunately such a theory must be a TOE, since you must exclude any possible force. There is no single way of establishing that a system is inertial without referring to the fix stars reference system, and indeed this is what we do all the time. Einstein was well aware of this issue, and he was Machian at the beginning, and believed that his GR being Machian would have solved the problem. But, unfortunately, GR is not really Machian.
As most cosmologist admit, we have a preferred frame: the background radiation.
The issue of inertial frame makes the notion of inertial mass circularly defined. The second book of Max Jammer on mass provides a very thorough history of all attempts in defining inertial mass, all of them failed, for various reasons. Jammer concludes that there is a logical gap between kinematics and dynamics, and which can be closed only with a kinematical definition of inertial mass.
Quantum Theory does not have such a huge foundational problem. The logical apparatus is complete and coherent. Moreover SR can be derived as emergent from QT (and this is now proved), whereas nobody in my knowledge ever succeeded in doing the converse.
Cheers
Mauro