One particular facet of this controversy that doesn't seem to have been explored in depth is the tremendous problems Shugden practice creates in terms of the Tibetan Buddhist pantheon.
In its early days, Shugden was seen as a minor protective deity on a mundane level. As such a deity, there were certain mediums who acted as oracles - similar to many others in Tibetan Buddhism.
However, when, for political reasons, conservative members of the Gelug establishment tried to elevate the status of Shugden to that of a Buddha, a seemingly minor mascot of fundamentalism began to threaten the entire deity “hierarchy”.
If Shugden was a Buddha, how could it manifest through oracles (this was always taught to be undesirable and impossible).
If Shugden manifested through oracles, why couldn't other Buddhas, like Tara, Chenrezig, Padmasambhava etc?
If HHDL and other lamas had allowed this to continue, this is exactly what could have happened. A bunch of mediums purporting to channel “fully enlightened” deities. And now you see the very truth in the Dalai Lama’s statement - that Shugden could cause Tibetan Buddhism to degenerate into “mere spirit worship”.
Now perhaps the NKT will say that Kalsang Gyatso doesn’t rely on oracles. That may be true, NOW (we know his uncle, a Shugden oracle, performed trances in order to give advice from Shugden to NKT as recently as the late 1990s).
Some may argue that other Tibetans also rely on oracles, but these oracles have never been considered to channel “Buddhas”, only oath-bound protector deities. So, one can see this very important distinction means that these oracles are not considered infallible, whereas the Shugden oracle is.
It therefore doesn’t take a PhD in Buddhist history to realize the tremendous problems Shugden presents for the authenticity of the Buddhist pantheon, not to mention taking into account the history of sectarianism associated with it.