In my opinion, the institute is more crucial than the branch as academics rarely matter for an IITian. What actually matters is how the college molded him from a fresher to a mentally stable and talented person who has honed his talents to the fullest through maximum exploration.

That being said, I would recommend you to go for IIT Bombay irrespective of the branch you are able to make it into. 

• IIT Bombay has its own legacy of being an IIT from the start whereas IIT Roorkee was a State University initially. Hence it is still undergoing changes. This eventually limits the opportunities offered to the students especially related to research work. At IIT Bombay many universities and R&D labs approach students for internships. 
• The rules for girls and boys are equal at IIT Bombay, unlike IIT Roorkee which discriminates between the 2 genders. 
• Because of its location, IIT Bombay, the finance capital is preferred over Roorkee. 
• The placements are better at IIT Bombay Civil than at IIT Roorkee Electrical, so need not worry about jobs. 

Overall, IIT Bombay will give you a sense of freedom to explore everything and broaden your opportunities.

It’s difficult to get into IIT Bombay MSc Applied Geology because half of the seats are reserved and the intake is also very less. 

As far as IIT Roorkee’s Applied Geology is concerned, don’t even bother going there. The faculty is very laid back with zero interest in teaching. The courses are taught with no practical approach and everyone can be found rote learning the concepts. No practical exams are conducted.

Academics

• The lab lectures are boring with no one to even teach sometimes and students waste their time there.
• Sometimes the subjects were taught via PPTs which were just played without any explanation.
• Math professor who had a Ph.D. in some math-related subject was the only one interested in teaching.
• The particular department has no learning environment.

Career prospects

• The career prospects are bleak for this department.
• Only 1 or 2 companies offer internships to earth science students at IITR
• Most offers are open to the integrated 5-year Geotechnology and Geophysical Technology students also who are preferred over the juniors obviously.
• Looking at the past records, non-placements or internship offers were made to these students

Anyone with a genuine passion for Geology should refrain from joining this course. Those who are after the IIT Tag is welcome to join it though.

To draw a better comparison, let’s differentiate IIT Roorkee and IIT Mumbai on the basis of branches 

CSE- On the basis of the research output, location, and popularity, Mumbai is the winner in this case while Roorkee stands in 4 or 5 positions.

ECE/Communications/Signal Processing: IIT Roorkee and KGP are the most preferred IITs. But considering the job opportunities, IIT Mumbai is again a winner.

EE: IIT Delhi's Electrical Engineering is considered the best-rank department internationally among other IITs. Mumbai and Roorkee are equally good but IIT Bombay again is slightly at an advantage. 

Mechanical: Madras and Mumbai are the best. Roorkee is also decent but yet not at par with IIT Bombay standards.

Chemical: IIT Bombay has an upper due to its better research output and the number of practicing chemical engineers.

Physics: Applied science is definitely better at IIT Roorkee. Even though its research and lab quality is comparable, however, IIT Bombay is preferred owing to the diversity in handling research problems.

Mathematics: In this case, IIT Kanpur takes the lead followed by Roorkee and Mumbai.

Chemistry: IIT Bombay is the best in every aspect.

Civil- IIT Roorkee’s Civil is considered the best in Asia. 

Space Sciences: Owing to its collaboration with ISRO, IIT Roorkee is the best.

Manufacturing: Although IIT Roorkee is decent when compared to BITS and KGP, it’s below average.

I believe IIT Bombay has a better campus life than IIT Delhi. Here are a few points to prove the same

• Events: Asia's largest technical event Techfest and cultural event Mood Indigo are organized by IIT Bombay. These are much superior and better than IIT Delhi’s 'Tryst' and 'Rendezvous' in terms of planning, entertainment, and scale.
• Transport: IIT Bombay has its own elaborate bus service inside the campus that runs 24/7 on CNG. IIT Delhi on the other hand just has 3-4 buses that run not more than 4-5 times during morning and evening. Hardly all the students are able to avail of this service because the buses are always fully occupied.
• Exotic Powai Lake: The hostels of IIT Bombay especially H12 and H13 offer a picturesque view from the balcony or rooftop and give a calming effect to the students conducive to learning. IIT Delhi on the other hand is located in the most polluted city and the hostels offer a similar unhygienic view.
• Restrictions: IIT Bombay has no rules regarding girls' and boys' hostels and students are free to visit opposite-gender hostels. IIT Delhi gives no such relaxation and gender mix is possible only during House Day, which is held once a year.
• Food and refreshments: IIT Bombay has an abundance of food and refreshments offered through kiosks, food stalls, and ice cream parlors. Although IIT Delhi too provides snacks, its food is not comparable to IIT Bombay.
• Mess food: IIT Bombay serves both non-vegetarian and vegetarian in their real sense whereas IIT Delhi caters to North Indians' taste buds mainly and the quality of food is also lower than IIT Bombay.

Some might find the above differences too minor, for them, it’s better to choose the one that aligns with their own preferences like location, etc.

Placement-wise, IIT Bombay is clearly the winner, followed by IIT Delhi with IIIT Hyderabad and BITS Pilani almost similar 

Courses: Course-wise too, IIT Bombay wins the race accompanied by IIT Delhi, IIIT Hyderabad, and BITS Pilani subsequently.

International competitions: The order remains the same except BITS scores better than IIIT Hyderabad in this aspect.

Startup culture: The startup culture too is best at IIT Bombay, then IIT Delhi followed by BITS and Hyderabad.

\Alumni: IIT Bombay has the highest number of successful alumni across the globe after which stands IIT Delhi, BITS Pilani, and finally IIIT Hyderabad.

I don’t think it’s logical to compare extremely old and government-funded IITs with private institutes like BITS and IIIH. The alumni reach is also incomparable.