I got computer science and engineering at UC Merced and data science at University of San Francisco with aid. USF will still be costlier that UCM. Which one is better respected for computer science and has better career options?
USF will be better - Merced too knew.
But guess what - if you have a CS degree, it can be some Easter Atlantic Ocean U. No one cares. You’ll have to pass a code test, etc. for the company.
Save the $$ - neither school a home run. Yes, USF will have more connections but go to Merced, save the $$ - you’ll be fine.
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Uc Merced + CS will get you a job, will be the experience of a smaller, new-ish, residential campus, and is cheaper. Go to UCM, excel, have fun, and take advantage of everything.
Cs/cse students are in high demand and if you have little to no debt you’ll be able to choose whatever job you like best then actually use&enjoy your salary instead of paying back a loan.
If you have extra money laying around, place it or invest it for 2025 as launch money.
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USF is not very known even in the Bay Area. UC Merced is a UC - and should be fine. Especially with CS.
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That’s debatable. I’m a native and I’ve never known anyone to NOT know the University of San Francisco.
Me (almost) 
. OK - it is debatable and apologies for the hyperbole - but it is not as well known as the other Bay Area universities: Santa Clara Univ, SJSU, SFSU, UCSC, Stanford, UCB, CSU East Bay, etc.
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Take a look at the CS curriculum for both schools and the course offerings. One school might have an emphasis in an area of interest vs. the other.
CS/CSE is highly employable so find the campus which fits you financially, academically and socially.
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Stanford and Berkeley? OK, you got me there. The rest, in regards to being “known,” is also debatable. My own D21 was accepted to Santa Clara and we ran into a neighbor who didn’t know there was a U in Santa Clara. 
But the OP wants to know about UC Merced and USF. USF gives a lot of merit money, so I’d say it depends on the $. USF has pumped some money into their campus with new dorms being opened this Fall. And location-wise, SF hands down.
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USF is not known as a strong CS school. UC Merced is a UC - they get that gold seal. This campus is also on the upswing! Once the medical school pumps out a few graduating classes, the entire school’s reputation will continue to go up. They are already a top 100 I believe.
As for CS - the theory is the same no matter where you go. Dive head first, swim hard and learn. THEN, also be super active in getting interships. Work with the profs, the job services department, and also do your own LinkedIn networking. ANY decent school + a good GPA + CS is a great career start. But, it all depends on the six inches between your ears, all the rest is just infrastructure around you.
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I agree there are pros and cons. I like UCM curriculum more - seems very strong on foundational aspects like math and science but still with good emphasis on coding and modern electives. location for USF is great particularly as we live in San Jose. Merced is not far either. I am hoping UCM will be bigger name in time to come - even may be by the time I pass out considering it’s has jumped very well in ranking in last 4-5 years.
Personally I also agree that UCM is probably known better than USF as I was not aware of them until last year.
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It’s a no brainer. The difference is $13k per year in-state vs $50k per year. Ignore “rankings” and “reputations,” they’re nothing more than subjective opinion. There’s no good reason to pay $250k for a degree as ridiculously employable as CS. You’ll be fine at UC-Merced.
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In my case, with aid from USF, I think difference is more like 10 to 15k. But yes, I get your point.
UC Merced’s reputation is only going to get stronger. They also seem to have really invested in relationships between professors and students (more so than other UCs). Of course, you’ll be in Merced . . . but unless that is the only thing you are considering, UCM seems like the obvious choice.
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I would say USF has a reputation similar to SF State or San Jose State in the Bay Area. My wife went there. But reputation isn’t something I’d base this decision on. In this situation, it makes more sense to go to Merced because of the cost. I’m also starting to get the sense that all the hype about data science is slowly fading.
Interesting that you think data science hype is fading! I also have some reservations about data science for undergraduate. CSE will definitely be stronger program to do for undergraduate and data science can be done as master dep do g on how it goes. I also have impression USF is likely known better for their graduate data science program than undergraduate.