Which choice is better: Jadavpur University CSE or IIT Bhubaneswar ECE?

It is up to your interest which domain you want to go in. But If you were comparing both on just placement perspective, CSE offers much higher packages from companies compared to other branches. 

• Course: CSE at Jadavpur University is quite good and as JU is situated in a metro city majority of IT companies visit the campus for CSE placements. ECE from IIT Bhubaneswar is said to have good academia and help you to shape the future both in IT as well as in the core sector.
• Infrastructure: Most of the IITs are equipped with the latest machines in their laboratories, and IIT Bhubaneswar has the same facilities. Students are learning from the new permanent campus and the hostel accommodations are good. Jadavpur University lacks a little behind IIT Bhubaneswar in terms of infrastructure.
• Exposure: IIT Bhubaneshwar provide opportunities even in the ECE course and IIT also gives you brand name which has its own advantages. However, the placement report of 2019 reveals that CSE students got 100% placement with an average CTC 19.96 LPA in Jadavpur University. The first ECE batch of IIT Bhubaneswar graduated this year so there is no past placement record for this branch, however, in 2019 there were overall 90% placements with an average CTC of 11.4 LPA.
• Environment: IITs provide an excellent infrastructure and college environment as JEE finds the best students for engineering. Also, the professors are highly qualified in IITs. Overall, the learning environment in IIT Bhubaneswar is better when compared to Jadavpur University.

If most of these factors are considered, ECE in IIT Bhubaneswar seems to be the better choice.