Both institutes are the same regardless of the branches. The same package of 3-4 LPA is offered at LNCT Bhopal and Vaishnav Indore.

Check the following points before making a decision:

• Know thoroughly about both branches and choose the branch where your interest lies. You will be offered different job profiles. 
• Data Analytics requires Mathematics, especially statistics intensely. Do not choose this branch if you are not good at it. 
• The average salary in major IT companies like TCS, Wipro is 3-5 LPA while Data Scientists are offered 5-7 LPA.
• CSE has great opportunities all over the country while Data Analytics is still a new program. It will not be worth it if you join an IT company as a Data Analyst. 
• You will learn programming languages like Python, R, SQL, PIG in Data Analytics while CSE will teach HTML, Java, C++, and PHP, etc.

You should go for CSE at LNCT Bhopal as it is more recognized and reputable. If you are interested in Data Analytics, then you can choose it as a specialization in plain CSE.