Why is there debate about thymus being an endocrine gland?
In my mind as an immunologist, there is no debate. In order to be part of the endocrine system, a body structure needs to be a gland that secretes one or more hormones to induce signaling at distal targets. These hormones can have multiple chemical forms. However, the thymus does not do that. It was proposed beginning back in the 1960s that the thymus contained and produced something called thymosin, which was eventually separated in 40 separate substances, none of which acts as a hormone, and most of which are now known to be present in many other tissues. T cell production and maturation occur as a result of signaling induced by cell-cell interactions (ligands and cognate receptors on the cell surface) as well as the action of many cytokines and chemokines. These compounds are not classified as hormones, though. 

It is possible that some hormones might be expressed in the thymus in very small quantities; however they are not secreted. This is due to a part of T cell development and maturation known as negative selection, where the thymus can ectopically express proteins typically only found in other tissues, such as the nervous system, pancreas, or lung, for example. This process allows for the removal of potentially auto-reactive T cells, which recognize self antigen.

Basically, knowing what we do about the function of the thymus in human and mouse, and how it does what it does, I honestly don't see how someone today could classify it as part of the endocrine system, even though histologically it may appear similar to glandular structures, and small traces of one hormone or another may be found in thymic extracts.