Colleges which are autonomous have the liberty to conduct any kind of exam the way they want so Autonomous colleges have an advantage over affiliated colleges.

While the colleges which are affiliated to VTU have to follow the same course structure as designed by VTU and examinations will be conducted for all the colleges at the same time.

VTU and autonomous won't differ much. What matters is faculty of college, facilities in college and more importantly PLACEMENTS.

So it depends on for which college you are going.