i've been researching shugden the last few days too. the obvious question is why would the dalai lama go against the core principle of Rime nonsectarian movement (which he claims to suopport), as well as the basic monastic vinaya discipline common to all sects of buddhsim in regard to creating sectarian division and causing friction and division among the sangha. In fact the dalai lama is the prime driving force in this division, it seems to me to be the case. Shugden is often said to represent the emanation of Manjushri himself. Furthermore, shugden is a protector diety of Dalai Lamas own personal lineage.
Needless to say, there is probably a very interesting reason for such a paradoxical ban.