I will take a little different tack on the OP’s list. The factors I am focused on:
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Doesn’t know for certain whether she wants to do a STEM major. This should be the MOST important factor in picking the school. Everyone knows of someone that got to their small “dream” school and realized they didn’t like their major and were stuck. She needs a school that is strong across academic disciplines.
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Wants a progressive vibe. I don’t want to have a political argument with anyone, but I would advise against going to most southeastern schools.
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Size of school. The OP said “a larger one that can feel smaller, or smaller one that can feel larger”. The first part of that quote can happen at most state schools. Young people will find their niche socially and academically pretty easily at most state schools. Going from small to large (like through a consortium) is a lot of work for the student.
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Test Optional - It is hard to handicap how schools will handle TO candidates over the long term. I would recommend finding a place to tell them that her test was cancelled three times and remove even the possibility that an AO thinks she is hiding a bad score.
Some thoughts on specific schools:
MIT and UChicago - these are very different schools from most and from each other. These two schools should probably not be on the same “Top 5” list of schools for an applicant. Unless your D really wants the unique MIT or UChicago experience, I would take both off the list. Also, MIT is probably not accepting a TO candidate.
I like Case Western a lot for your D. Yes, Cleveland is not pretty, but the few people I know of that sent one of their children to CW give it excellent reviews.
The UCal admissions process is probably worth its own message board given how opaque it is. The schools themselves are excellent and I think would all be a good fit for your D.
I would drop Carnegie Mellon off the list. It is hard to move between majors at that school.
Boston University - good school, really fun location, but very expensive and not exceptional in STEM.
U of Rochester is a really good option for your D, as others have pointed out. Not easy to get into, but definitely a more “nerdy” environment and demanding academically.
Brown has a bit of a reputation as the “easiest” Ivy academically, so it seems like every 4.0 kid in the country that wants to take it easy in college applies to it. If your D is looking for a rigorous academic environment, this may not be it. There is also a huge advantage to applying ED, so if this is not your D’s “dream school”, then it is going to be really hard to get in.
Some more match or low reach options that are not on the list:
U of Wisconsin - Very good school across academic disciplines, and and a very good fit for your D culturally. Winters in Wisconsin are long and cold, but I think your D would like this school. I strongly recommend checking it out.
Utah - culturally a unique school, but strong in STEM and offers a wide range of academic options.
U of Michigan - I have never met someone who went to Michigan that did not love the school. Strong across academic programs. A little pricey for out of state.
U of Washington - plenty of rain here. Good school, progressive culturally.
One of the things about the good state schools is that there are a gamut of students. If your D wants to play D&D and just “nerd-out”, she will have no problem finding people into that at any of the better state schools. If she wants a demanding academic environment, she will definitely find that in the more challenging majors at the states. There are also more goof offs and slackers at the state schools, but those kids are often a lot of fun to hang out with.