Does not the Dalai Lama decide what is practiced by Gelugpas?

In reality, the Gelugpa spiritual leader is Ganden Tri Rinpoche who is the throne holder of Je Tsongkhapa. The Kagyupa spiritual leader is Gyalwa Karmapa, the Sakyapa spiritual leader is Sakya Trizin, and during Dudjom Rinpoche’s time he was the spiritual leader of the Nyingmapas. These spiritual leaders have responsibility for the development of their own tradition in their monasteries, communities and Dharma Centres. Of course Ganden Tri Rinpoche should have responsibility for the development of the Gelug tradition in general, but at this present time he is powerless. I do not believe that it is Ganden Tri Rinpoche’s wish to ban the practice of Dorje Shugden. Even if Ganden Tri Rinpoche was in control of the development of the Gelug monasteries, he would still need to discuss his ideas with the majority of monks. He could not make unilateral decisions. In any case he could never control individual practitioners, they always had the freedom to choose and maintain their own personal practices.

For instance, although Sera, Ganden, and Drepung (in Tibet) were Gelug monasteries, many Nyingmapa and Bön practitioners joined to study the philosophical teachings. In my class in Sera-Je I had some friends who were from a Nyingma monastery in eastern Tibet. Their daily practice was Nyingma, and no-one was unhappy about this. They had complete freedom. We never had any problems because the abbot gave complete freedom for individual practice. (Geshe Kelsang Gyatso, talk.religion.buddhism, 19 December 1997)

HH the Dalai Lama says: “That cult is actually destroying the freedom of religious thought. Say I want to practise Nyingma. They say this Protector will harm me.” This is also completely untrue. We would like to ask HH the Dalai Lama: who are these Shugden practitioners saying these meaningless things? His words are causing disharmony between Shugden practitioners and Nyingma practitioners. Why is HH the Dalai Lama creating this new problem? Until now there have been no problems between Gelugpas and Nyingmapas, and there has been no arguing or criticism. Some scholars debate with each other, such as the well-known Gelugpa scholar Yonten Gyatso and Dongthog Tulku, a scholar from another tradition, who conducted a debate by letter over a number of years. They have written many books replying to each other’s assertions, but this does not mean they are criticising each other. They are simply clarifying the doctrines of their own traditions, with good motivation. There is nothing wrong with this. I would like to ask: what is the problem between the Nyingma and Gelug traditions? There is none. The majority of people from both traditions naturally live in harmony, so why is HH the Dalai Lama destroying this harmony by saying things like “Shugdens say you should not even touch a Nyingma document”? Although we concentrate on our own tradition we respect all other Buddhist traditions, including the Nyingma, and we rejoice very much in their sincere practice. (Geshe Kelsang Gyatso, False Accusations Against the Innocent: Letter to the Editor of Newsweek, 05 May 1997)