Well, as you might have known that VIT Bhopal has new campus and so the faculties might not be as good as compared to the Chennai campus, so I reckon you can go for ECE at VIT Chennai campus as it's campus is also more well developed and infrastructured than that of Bhopal campus. But at the same time, campus doesn't matter if you're willingly going to take the course you are interested in since one should not sacrifice it's course field to study further.

Plus, since VIT is a prestigious private college of India, all of it's faculties must be at their best and obviously they are. So you can easily go to any of the either colleges taking any of the courses you're willing to without any doubt.

All the best.