Hello Dipanshu, 

First thing yiu need to understand is that, RTU is a university and GEC Ajmer is a college affiliated to RTU. 

So you will get the same degree on choosing any of the above college. The difference you may find in thw faculty, Infrastructure, Placements and other such factors. 

As per the ratings GEC Ajmer stands at 3.1 and RTU stands at 3.5 out of 5.

As per my knowledge, RTU is a much better institution for engineering because of its slightly better rating. Placements of RTU is much better the  GEC. You will find more experienced faculties compared to GEC. Industry exposure is also provided to the students in RTU.

So all in all, as per me RTU should be opted over GEC Ajmer. Rest is up to you.

Hope this helps  Thank You 

All the best