"Hoping the selective colleges she is looking at won’t see this as a problem. "
That would depend on the college and rigor that the other applicants showed, or if the adcoms think someone is ducking a hard class and not challenging themselves when they could have.
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She is clearly not trying to duck hard classes… just concentrating on ones that interest her more. Since she wanted to be able to take Physics E&M senior year she had to take Mechanics junior year, since it is a prerequisite. she was advised to take AP Chem right after honors Chem. She opted to take the AP Computer Principles course since she felt she has no background at all in computers. She has taken honors history classes her freshman and sophomore years and already done really well in those classes. Why does everyone need to take a History class to show rigor???