Which is a better option: IIIT Hyderabad (M.Tech CSE) or BITS Pilani (M.E Software Systems)? Why?

In my opinion, M.Tech in CSE from IIIT Hyderabad is way better than the M.E. Software System from BITS Pilani. Honestly, both the colleges are good so my comparison is only on the basis of the courses. Consider the following points of comparison 

• ME in the Software System curriculum mostly comprises software engineering or IT subjects and has little connection with the actual CSE curriculum. Whereas, if you take CSE, you can opt for the subjects of your choice from the second year and can take subjects directly related to CSE. 
• BITS Pilani has a better brand value and enjoys more global recognition than IIIT Hyderabad thereby making it easy to pursue Ph.D. from a foreign university.
• M.E. in Software Systems limits the scope of a Ph.D. with a good research area in CSE.

In the end, I will say both IIIT Hyderabad and BITS are excellent institutes for CSE education and offer equally good placements. So priority should be given to the course and not the college!