There are 2 other tulkus that you have left out, if I may point out. Taranatha is the founder of the Jonang School and not only was his incarnation banned in Tibet, the Jonang school which he founded was also banned but they went underground and survived. The current Dalai Lama's Kalachakra cycle of teachings comes directly from the Jonang School. Historical records of Tibet says that the school was closed down and deemed heretical, misleading and dangerous because of their view of emptiness known as shentong is opposite of what is taught by the Gelug school. However, the current Dalai Lama NOW admits that it was closed purely for political reasons. Taranatha subsequently reincarnated in Mongolia, where he is known as the line of the Jetsun Khalkas, and is to Mongolia what the Dalai Lama is to Tibet.
The other high lama whose incarnations was banned is Chankya Rolpa Dorje. He is the Lama to the emperor of China, Qianlong. There were no reasons given for the banning of his reincarnation, other than him being more popular and more wealthy than the government at that time. His reincarnation also reappeared in Mongolia and he is known as the line of Chankya hutukus there.
That's interesting to read about Taranatha and the controversial closing of the Jonang school. I am sure it was political and not because of its esoteric view of emptiness. If they are able to produce great and attained masters, I am sure their view of emptiness is just as valid although it may not conform to Lama Tsongkhapa's interpretation. It may be valid but it does not mean Lama Tsongkhapa's view is not valid. I still maintain that Lama Tsongkhapa's view as expounded in the Gelug School is superior because of Lama Tsongkhapa's special qualities and that his view was moulded and guided by Arya Manjushri. It is superior meaning it is a speedier method to achieve the correct view of emptiness.
Anyway, I became fascinated with Taranath and I did a bit of googling and came across this interesting bio:-
Taranatha Jetsun Taranatha: 18th cent, Amdo
Alternative Name(s): Kunga Nyingpo (Kun dga' Snying po), Jetsun Taranatha (Rje brtsun tA ra nA tha), Taranatha (Grol ba'i Mgon po)
Period: Later Masters (16th–18th)
Lifespan: 1575–1635
Sites Founded:
Takten Damcho Phuntsok Ling Monastery rtag brtan dam chos gling
Major Site(s) of Residence:
Former:
Great Stupa Mountain Hermitage jo nang sku 'bum ri khrod chen mo
Cholung Changtse Monastery chos lung byang rtse
Teacher(s):
Buddhagupta Sangs rgyas Sbas pa'i mgon
Literary Works Composed: 'Dzam thang Outline (PDF) Rgyal rtse Outline (PDF)
Annotated 'Dzam thang Outline (TBRC.org) Annotated Rgyal rtse Outline (TBRC.org)
Biography:
Jetsun Taranatha was born at Karag (kha rag) in the hereditary line of the great Tibetan translator Ra Lotsawa Dorje Drak. His Tibetan name was Kunga Nyingpo, but he is generally known by the name Taranatha, which he received in a vision from a great Indian adept. When he was about one year old he declared, “I am master Kunga Drolchok!” But this was kept secret for several years, and it was not until he was about four years old that he was brought to Kunga Drolchok’s monastery of Cholung Changtse and formally recognized as his incarnation. He then began years of intense study and practice under the guidance of a series of great masters, many of whom had been major disciples of Kunga Drolchok.
Guided by Kunga Drolchok’s disciple Jampa Lhundrup, Taranatha first studied and mastered various subjects of sutra and tantra. Then he received a vast number of tantric teachings and initiations, primarily of the Sakya tradition of Lamdre, from another of his predecessor’s disciples, Doring Kunga Gyaltsen. Kunga Drolchok’s disciple Dragtopa Lhawang Dragpa taught Taranatha many esoteric instructions, especially the Six Yogas and Mahamudra, which caused a sublime primordial awareness to arise in the young prodigy’s mind. Jedrung Kunga Palsang, who was Kunga Drolchok’s nephew and successor on the monastic seat of Jonang, transmitted to Taranatha the teachings of Kalacakra and the Dharma protector Mahakala that he had received from his uncle. From Kunga Drolchok’s disciple Lungrik Gyatso, Taranatha received many transmissions, especially the Kalachakra initiation, the explanation of the Kalachakra Tantra, the esoteric instructions of the sixfold yoga according to the Jonang tradition, and the collected writings of dharma lord Dolpopa Sherab Gyaltsen. He gained a special experiential realization when he practiced the sixfold yoga.
When Taranatha was fourteen years old, the Indian adept Buddhagupta-natha arrived in Tibet. This master became one of Taranatha’s most important teachers, passing to him countless transmissions of tantric initiations and esoteric instructions. Taranatha stated that his understanding of the secret mantra teachings was due to the kindness of Buddhagupta-natha alone. Several other Indian yogins and scholars, both Buddhist and non-Buddhist, came to Tibet during Taranatha’s lifetime, such as Balabhadra, Nirvanasri, Purnananda, Purnavajra, and Krsnabhadra. Some of them taught him profound instructions, scholarly topics, and joined him in translating Sanskrit manuscripts into Tibetan. Several of Taranatha’s translations are now included in the Tibetan canonical collections of the Kangyur and Tengyur.
In 1588 Jedrung Kunga Palzang, who had followed his uncle Kunga Drolchok as holder of the monastic seat of Jonang, enthroned Taranatha at Jonang, although a formal ceremony of investiture did not occur until 1595. Taranatha took upon himself the responsibility of causing the dharma lord Dolpopa’s insights to once again reach a wide audience. He was determined to revive what he saw as a priceless transmission lineage in danger of being lost. During the 1590s the instruction manual of Dolpopa’s dharma heir Chogle Namgyal was still being used at Jonang to teach the sixfold yoga, but very few people understood the philosophical tenet of Dolpopa and his spiritual sons. Taranatha was even more concerned that some of the previous holders of the monastic seat of Jonang had given initiations and instructions according to the Jonang tradition, but had also criticized and refuted Dolpopa’s vajra proclamations of the ultimate view of zhentong, which Taranatha felt was the secret teaching of all the buddhas and bodhisattvas. Even though he personally disavowed any ability to refute another system, he now felt the need to defend the original views of Dolpopa through refutation of erroneous opinions, and to establish the correct interpretations according to his lineage.
During this period Taranatha’s teacher Jampa Lhundrup advised him to restore the Great Stupa of Jonang that Dolpopa had built about 260 years before at Jonang. Taranatha put all his energy into the project. Just before the restoration work was finished, he had a marvelous vision one morning. The earth and sky seemed filled with countless people of all descriptions going in the same direction. He joined with them and arrived in a red, triangular valley with an incredible crystal mountain in the center. The mountain was totally filled with amazing stupas of different sizes, and in each stupa infinite buddhas and bodhisattvas were speaking back and forth about the dharma. Flowers fell from the sky like rain, and many other miraculous signs occurred. All of the people were making offerings to the crystal mountain filled with stupas, and chanting a series of verses in unison. Awestruck, Taranatha asked about the mountain, and was told that it was the Dhanyakataka Stupa, where the Buddha had first taught the Kalachakra Tantra. Taranatha later felt that perhaps this vision had occurred because everyone had been working so intensely to complete the restorations of the Great Stupa at Jonang.
In 1604, after a decade of efforts to revive the original Jonang teachings, all of Taranatha’s work was threatened by serious political conflict between the regions of Jang (byang) and Tsang. Jonang itself was in immediate danger of being attacked by hostile armies. While meditating at Dolpopa’s great stupa, Taranatha became despondent, and, seeing all his efforts about to be wiped out and the tradition itself perhaps destroyed, wished only to go into retreat far away from all the troubles created by deluded and impassioned people. But Dolpopa then appeared to him in a vision, encouraged him to continue as before, and assured him that his efforts would not be in vain. The next night Taranatha prayed to Dolpopa and experienced a vision of a bodhisattva who spoke a quatrain of verse. As a result of these events, Taranatha said he gained realization of Dolpopa’s true intentions as expressed in his zhentong teachings, and all his uncertainties and doubts were completely removed. He felt that a great key had been placed in his hands to open the doors of all the Buddha’s doctrine. As an expression of his realization he composed a versified text entitled, Ornament of the Zhentong Madhyamaka, which is one of his most important works solely devoted to the explication of the zhentong view. Taranatha said that he received several prophecies from Dolpopa, and thereafter met him many times, both actually and in dreams. He further commented, “That is the reason I am now an expert in the great omniscient Dolpopa’s view and preserve his true intentions.”
Taranatha had countless such visions during his life. For example, many times during the years 1618 and 1619 he experienced visions of the Kalapa court of the Shambhala emperors, beheld the rulers themselves, and heard their teachings. He felt that these visions were a result of his belief that the ultimate view of all sutras and tantras was zhentong Madhyamaka.
In 1615, the powerful Tsang ruler Desi Puntsok Namgyal provided a special piece of land and the necessary supplies and workers to begin construction of a monastery to serve as a center for the teachings of the definitive meaning of the Buddha’s doctrine. This monastery, which was finally completed in 1628, became Taranatha’s main residence and was known as Takten Damcho Ling.
Shortly before his death, Taranatha appointed his disciple Sangye Gyatso as his successor on the monastic seat of Takten Damcho Ling and made many prophetic statements about the Jonang tradition and the great political troubles that would soon sweep through Tibet. Unfortunately, Sangye Gyatso passed away not long after Taranatha himself. Thus another of the great master’s disciples, Kunga Rinchen Gyatso, was appointed to the monastic seat and led the Jonang tradition for the next fifteen years.
