What should I prefer, a dual degree in BITS Pilani or CSE in Thapar University?

I can only guide you but only you know what is right for you. If you are serious about a career in CS, Thapar University will offer better opportunities and an environment. But if you want to explore other things and also want to enjoy your college life, then taking a dual degree at BITS Pilani will be a great choice for you. BITS has a very flexible curriculum so it allows you to explore your ambitions thoroughly and openly. Moreover, you will be exposed to a better crowd and culture so obviously the learning experience will be more enriched. Generally, both institutes have their pros and cons, and going through these will guide you better toward making a well-informed decision. 

Thapar University Pros: 

1. You will be able to study CS, which has amazing job opportunities.
2. You will complete your graduation in 4 years
3. Excellent accommodation facilities at par with BITS

Thapar University Cons:

1. 75% attendance rule
2. The crowd and academic ambiance are not at par with BITS because of the reservation policy.

BITS Pilani Pros:

1. No compulsory attendance rule
2. The packages offered are great but you will have to work hard for them
3. More talented and skilled peer groups because of no reservation
4. Dynamic campus life

BITS Pilani Cons:

1. You will be completing your graduation in 5 years, a year later than your BTech counterparts
2. You will have to study extraordinarily hard in the first year to get the branch of your choice.
3. Intense competition and academic pressure.

Lastly, don't take dual degrees in BITS on the pretext of getting  CS. Only a handful of students get to choose CS in dual degrees.