More than a third of sixth formers lack motivation in their studies mainly because they have little control over their course options, according to an Assembly government survey.
The Schools' Learner Voice survey, published last week, concluded that students in Wales who follow their first-choice courses are much more likely to be satisfied and dynamic learners.
Almost 4,000 young people in Years 10-13 took part in the survey, which examined general attitudes towards education and the vocationally led 14- 19 learning pathways initiative.
Most pupils reported that they were happy with the standard of education and the quality of teaching they received.
About 70 per cent of Years 12 and 13 students rated their teachers as "fairly good" or "very good" for their support, listening skills, good use of lesson time and their ability to explain the subject.
In 2008, more A-level students were following their ideal course than five years ago, the survey said, but it concluded that options were often limited by "timetabling problems" rather than the availability of specific courses.
The report found there was a "clear correlation" between whether a student was studying their first choice of subjects and having problems.
Students studying at their preferred school also said they were more motivated and less likely to think about dropping out.
Girls were also found to be less likely than boys to have been advised by teachers not to pursue their preferred courses.
The report said targeted support should be given to students, particularly those from ethnic minorities and those at small or rural schools, who are less likely to get their first choice of course or subject.
"Perhaps the important issue demonstrated is that no course type is immune from disenchantment and support systems need to be in place to capture vulnerable students," it said.
From 2012, every school will have to provide students with at least 30 distinct courses to choose from, including a range of vocational options.
According to the report, one-fifth of Year 10 and 11 pupils studying the Welsh baccalaureate said they felt "very motivated" compared with just 8 per cent of those doing GCSEs or NVQs.
But GCSE students taking some lessons outside school were less satisfied with their education than those studying in-house, and were less likely to want to continue to Year 12.
The support of teachers and careers advisers was crucial for improving pupils' prospects and self-confidence in making good decisions, the survey found.
The report said: "Emphasis should be placed on creating awareness among students and their parents of the expertise, credibility and impartiality of Careers Wales and teachers. This should be initiated well before crucial decisions in post-14 education are taken."
Support from parents was also highlighted as an important factor in pupils' decision-making.
One-third of Year 10 and 11 pupils said their parents had influenced their subject choices.