Thanks for A2A. The question you have asked is very relative and it may sound that either of the options that you put forth seem to be correct. Let us analyse both the scenarios for you.
When I was in a position like yours last year, it was tempting for me to decide whether I wanted to study EEE at MSRIT or study CSE at KJ Somaiya college of Engineering, Mumbai. The reason I went to KJSCE was that I had a penchant for Computer science and KJSCE was as prestigious college in Mumbai as MSRIT is in Bangalore giving ample opportunities to its student by way of a sprawling campus, good faculty, clubs, festivals, learning environment, etc. Hence I decided to go to a lesser good college(Only marginally not good as compared to MSRIT) and pursue CSE instead of EEE.
If you are in a position right now that you have to sacrifice the branch you like and opt for a different branch which you are getting in an esteemed college and the college in which you are getting the branch you like is extremely crap(When I say the word crap I mean it. It doesn’t have everything which I mentioned in the above paragraph), then go for preference by college.