Pune University is better in terms of syllabus, exposure and examination pattern.
PU is more recognized. So, you will get better exposure, if you are planning on pursuing higher studies.
Having known some people studying in both Pune and Mumbai university, I can say why Mumbai University is a better place to study engineering than Pune University.
Each year, a large number of students from both universities apply for MS programs at international universities. However, Mumbai university has a higher number of selected students than Pune university; hence Mumbai university has a stronger global exposure than Pune university.