Academics from the universities of Staffordshire and Manchester found high levels of aspiration and optimism among those in mainstream schools. They talked to more than 1,000 pupils with emotional and behavioural problems and moderate learning difficulties, and their parents.
Those in special schools were also less likely to aspire to higher level academic courses, and less sure about what courses they wanted to follow.
They were also more likely to continue in post-16 education in the school they were already attending, while those being educated in the mainstream sector tended to want to go out to work.
The study found children educated in mainstream schools wanted to lead independent lives as adults. They wanted skilled jobs, while those in special schools opted for manual work.
Teenagers from mainstream secondaries were also more likely to spend time with friends outside school, suggesting they are more socially integrated.
The report concluded that the Government should provide "substantial financial incentives" to schools to enrol special needs pupils because of the positive effects of mainstream education on their lives and associated savings on additional support, such as the Connexions service.
The findings came as a report by Cambridge university for the National Union of Teachers claimed that mainstream schools were not equipped to deal with pupils with special needs. Staff lacked appropriate training and as a result often left themselves vulnerable to legal action if things went wrong.
While many teachers supported inclusion in principle, they were concerned about the lack of support for children with behavioural and mental health problems. The report said the greatest difficulties were in the most disadvantaged areas where "a critical mass of un-met needs... overwhelm school staff and create a downward spiral of achievement."
Steve Sinnott, general secretary of the NUT, said: "It is necessary for the ideal to be practical. In order to work it has to be properly resourced..."
* The influence of schooling on the aspirations of young people with special educational needs www.bera.ac.uk
* The Cost of Inclusion www.nut.org