This is an interesting section on the Wikipedia page about Geshe Kelsang Gyatso with regard to his views of the current state of the Gelugpa tradition.
Relationship with Tibetan politics
Consistent with the lineage teachings he received from his root Guru, Kyabje Trijang Rinpoche, Geshe Kelsang believes that the practice of Dorje Shugden should continue to be practised by any Gelugpas who wish to do so. This view differs from that held by the current Dalai Lama, who, despite having received the same lineage teachings, now actively discourages this practice. However, as it is an independent Western Buddhist organization, the Dalai Lama has no authority in terms of how the NKT-IKBU is organized and what practices are taught. The controversy surrounding the Dalai Lama’s ban of the practice of Dorje Shugden is described in the article on the Dorje Shugden Controversy.
Geshe Kelsang said at an NKT-IKBU Festival in 1995 that the Gelug tradition is in a state of “serious degeneration.” In explaining this, Geshe Kelsang said that if the Dalai Lama succeeds in destroying the practice of Dorje Shugden, the entire Gelug tradition itself will be destroyed:
If the practice of Dorje Shugden is harmful then it follows that Je Phabongkhapa was not an authentic Buddhist master, and if he was not then there is no doubt that his heart disciples, Kyabje Ling Rinpoche and Kyabje Trijang Rinpoche (the Senior and Junior Tutors of HH the Dalai Lama) were also not authentic. These three Lamas are the most important Gelugpa Lamas of recent times. If these three are not pure Teachers then there is no doubt that the entire practice of the Gelug Tradition is invalid. This is the main issue that needs clarification.
Geshe Kelsang become critical of the Gelugpa hierarchy’s attempts to prevent him from passing on Dorje Shugden teachings that he had received from his own teacher. The distancing of Geshe Kelsang from the Tibetan hierarchy has also been underlined by a number of revisions made to later editions of his earlier publications. Geshe Kelsang’s dedications to the long life of the Dalai Lama found in earlier editions of Meaningful to Behold are omitted from the fourth edition (1994) onwards. Also, Geshe Kelsang’s students made revisions to the list of Mahamudra lineage gurus in the second edition of Clear Light of Bliss published in 1992. (On this point, Kyabje Gehlek Rimpoche explains that “We have two lineage prayers, one long and one slightly shorter one. Geshe Kelsang Gyatso, who had the teaching from Kyabje Trijang Rinpoche at the same time when I was there, gives the shorter lineage prayer and I put in the longer one.”) In the first edition, Phabongkha Rinpoche was followed by Trijang Rinpoche and Ling Rinpoche, the latter being the ‘current holder of the throne of Ganden’. In the second edition, Ling Rinpoche’s name is omitted and replaced by ‘Dorjechang Kelsang Gyatso Rinpoche’ (Geshe Kelsang Gyatso).