"The theory of relativity is considered to be self-consistent, is consistent with many experimental results, and serves as the basis of many successful theories like quantum electrodynamics. Therefore, fundamental criticism (like that of Herbert Dingle, Louis Essen, Petr Beckmann, Maurice Allais and Tom van Flandern) has not been taken seriously by the scientific community, and due to the lack of quality of many critical publications (found in the process of Peer review) they were rarely accepted for publication in reputable scientific journals. So, as in the 1920s, most of the critical works have been published in small publications houses, alternative journals (like "Apeiron" or "Galilean Electrodynamics"), or private websites. Consequently, where criticism of relativity has been dealt with by the scientific community, it has mostly been in historical studies.
However, this does not mean that there is no further development in modern physics. The progress of technology over time has led to extremely precise ways of testing the predictions of relativity, and so far it has successfully passed all tests (such as in particle accelerators to test special relativity, and by astronomical observations to test general relativity). In addition, in the theoretical field there is continuing research intended to unite general relativity and quantum theory. The most promising models are string theory and loop quantum gravity. Some variations of those models also predict violations of Lorentz invariance on a very small scale." (http://en.wikipedia.org/wiki/Criticism_of_the_theory_of_relativity#Status_of_criticism)
So I would say its only "shortcoming" is that it has yet to be unified with others theories, yet since it is self-consitent, that isn't really a shortcoming of GR.