Yes, the foundation of Mahayana Buddhism lay indeed in Gandhara; this is also how Buddhism was transfered into central Asia and China later on. The Ch'an lineage in China was founded by Bodhidharma, a Gandharan monk. We can also trace back the lineage of the Shingon sect in Japan to two people; Kukai (who is refered to in Shingon Buddhism as Kobo Daishi or O-daishisama) was schooled in the ways of esoteric Buddhism (known as mikkyou in Japan) by a Chinese monk, Hui-kuo as well as Gandharan scholar by the name of Prajña (which means "wisdom" in Sanskrit).
This Prajña is also reported to have taught Kukai the Sanskrit language and Vedic scripts. Interestingly, the Shingon sect is the only live Buddhist school to still use Sanskrit writings. If we take a look at the Daibutsu of Todai-ji, an important Shingon Buddhist temple, we'll notice that his style of clothing is not east Asian at all:
Of course, Kukai traveled to China in the 9th century, which was way after the destruction of the Indo-Greek and Gandharan kingdoms,but I think the Islamic caliphate had already incursed into Afghanistan by then. Actually, something that is remarkebly interesting is the fact that the Buddhists of Gandhara suffered a lot under the rule of the Kushans, and were probably pushed out after the Hindu Gupta empire took over. However, the Gupta empire extended just to the Indus river, and the Sassanid Empire, which had been quite tolerant of Nestorian Christians, Jews, Hindus and Buddhists in their early rule, had not established control of Gandhara. Even at their greatest extent, they did not control the area from Kabul onward.
Interstingly, the Sanskrit word for Kabul is "Kamboj"; remember the Kambojas? They are mentioned several times, and Buddhist sources conflict here (King Ashoka has sent missionaries to convert them, which they apparently did, but other Buddhist scholars noted that they killed insects as a holy duty, thus breaking the first of the Five Precepts (I vow to undertake the training not to kill a living being)). Apparently, an amount of them did convert at one point from either Zoroastrianism or Hinduism, but certainly not all.
What we can agree on, probably, is the fact that the Buddhist clergy and population, being pushed out (either voluntarily or under pressure) of the Gupta Empire, would have settled west of the Indus river, inbetween the Sassanid and Gupta Empires. This would have been an excellent location for Buddhism to mingle with Indo-Hellenistic culture; and forming an interesting mix there, which might have led to Mahayana Buddhism!
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