The future of the Gelugpa Vajrayana tradition will endure. Dorje Shugden is the Protector of our lineage and as we believe and trust in him, I do believe that our lineage will continue. Perhaps it might evolve to suit the times ahead. Perhaps it might even change into a new school, but the core is that Dorje Shugden manifested to protect Tsongkhapa’s teachings and thus the Gelugpa lineage, and all of us here who say that we are Dorje Shugden practitioners should not lose sight of that.
Gelugpa is a living lineage, with masters that are still alive. There are various Gelug lamas these days who take on an unconventional approach to planting the seeds of Dharma in the minds of people such as Segyu Rinpoche, Lama Osel and Gomo Tulku. And there is nothing wrong with that even if the methods differ from Lama Tsongkhapa's, as long as the message gets across. Even the current Trijang Rinpoche is teaching and training students as a lay lama as opposed to as a monastic but it does not change his attainments and his realizations, not even one bit. And I believe here in this forum, none of us doubt the attainments of these masters. Starting another lineage or splintering from the main lineage could actually be an alternate method of spread the Dharma, if things in the main lineage become too hairy for some reason and these masters wish that their disciples not be affected which is why they had to split. This is how id like to see it anyway. In a traditional sense, splitting from a monastery or lineage is a very bad thing, but sadly, during times like these, things have to manifest the way that they appear to be, for now.
The Gelug lineage that has been passed down to Pabongkha Rinpoche is still intact, and we still have all the teachers who hold the full transmissions from Pabongkha Rinpoche and they are thriving despite the political issues that surround them. The Dharma protector is alive and real, and he will protect the lineage and prevent it from degenerating. If we doubt even this, then we are saying that Dorje Shugden does not exist. If we worry about Gelug's future, then we are directly doubting Dorje Shugden's vows, ability and power because he has promised to protect the Gelugpas, and him failing to do so means that he is ineffective. I say that we should have trust in our protector. After all, he has never failed us.