Whether you consider the nature of gurukula or schools run as communities headed by gurus (also known as ashrams) as advantages or disadvantages for the pupils really depends on your point of view. Before the advent of British rule, these were the major types of schools in India and an essential part of the Hindu tradition.
The students (shishya) in the school did not pay fees but did chores around the schools such as washing and cooking and cleaning. Rich and poor students, because they did not pay fees, were treated equally. The facilities were generally quite minimalistic, as the students were expected to be learning to do without luxuries. During their time at school, students were separated from their families and placed under the strict authority of the guru leading the school. Whether you consider this sort of austerity and hard work an advantage or disadvantage really depends on whether you think that children should learn to work hard and take care of themselves or not.
Another disadvantage is that the quality of the school depends to a great degree on the individual guru; it isn't monitored by some sort of independent authority, which can lead to the abuse of power.
Unlike in the modern period, there were no formal schools in the vedic period. Some of the disadvantages were:
1. Discrimination in the admission.
2. Students have to remain confined to the gurukul and get no exposure to the outside world.
3. There was no prescribed format of education and evaluation. Students were taught the skills and education possessed by the gurus only.
4. Students have to leave home at an early age, which deprived them of the parental love and care.
5. Students have to obey the gurus and have to strictly follow the rules of the gurukul without any argument.