Raistlin actually posted this over in a thread in the FFXIV forum, but it seems particularly relevant here and may provide insight that could confirm some suspicions here in this thread.
In a recent financial report the Chief Financial Officer Yosuke Matsuda discusses the negative effects from Final Fantasy XIV's disastrous launch and the financial consequences throughout the company. Last year the operating budget was halved as a consequence of how much money Square Enix has been bleeding, and Matsuda identified this as a cause of the delay in the release of many HD titles. The success of Final Fantasy XIV has become so immensely important that it really does seem that almost all of Square Enix's available in-house development resources are being fueled into A Realm Reborn.
Obviously this does not explain the entirety of Versus XIII's delays, but it certainly accounts for the near radio silence over the past two years.