I mean, basic property rights should generally be respected, unless there is a compelling public need for such a collective use of such property - and obviously in no instance should the government take away someone's land based on their ethnicity.
Is that actually what happened in Sikkim?
No, that is not what happened in Sikkim. There is no proof of that and I don't think Simfan or Politicus would disagree with me.
I can understand their point of view as well. It really depends on whether you think being connected with the outside world is a good thing or not. Is it a good thing that Bhutanese students will never have a chance to attend an IIT and get a well paying job connected with the outside world, or even get to visit/work outside of the subcontinent? Of course being connected with the rest of India also has its disadvantages. There are a lot of pros and cons to weigh.
Also, it should be noted that many of the states in the northeast of India have a lot of autonomy and that is a good thing. And the party in power right now in India is a strong proponent of federalism, including in the northeast (look at the alliance past and present of the BJP). For example, in Meghalaya, even in the capital of Shillong, one cannot buy property without proving that both their grandparents are from Meghalaya. That is the opposite of the local people not having control over their land. Rather, they are allowed to exclude people from their lands, and it is allowed by the Indian government.
Also, many of the separatist movements still left in India are located in the hilly area of Assam. That is because the plains of Assam are populated by the Assamese people and they overwhelmingly dominate the culture and politics of the state as opposed to the tribal people of the hills who are more similar to the Nagas, Khasis, Garos etc. The separatist movements in the other states have mostly died down with greater autonomy. As far as I know the people there are pretty ok with the current situation where they can control their own states. And in any case they are much better off than the people in Bhutan or Tibet.......