Which one is better to choose between Kalyani Government Engineering College and University of Calcutta for the WBJEE, if one cant get Jadavpur University?

If you solely consider studies as the basis of the selection of an institute for your career, I don't believe there will be much of a difference. 

• The chief difference arises because the colleges were established at different times. 
• As time goes on, new clubs emerge at institutes that improve with time, the festival improves, and norms and culture unique to the college change over a period of time. 
• Because CU's engineering programs are newer, they may have certain disadvantages for several fields. 
• You may claim that you are unconcerned about everything other than your academics, but once you enroll in a college, you will realize how vital everything is. 
• Kalyani College does have a far larger student body than CU, you will have a diverse group of students in your batch. 

Also remember, that usually everyone despises their own university no matter how good or bad it in reality is. You surely would not want a gloomy college experience. So do your homework before deciding on an institution.