I thought this was interesting, though it’s already 15 years old:
We’re not talking about (the OP) being a random kid without access to good courses. I thought the focused question was how his application would look if it was unbalanced in the sense of 3-4 each advanced physics/math classes and no AP Chemistry. This would indeed be a “holistic review”.
The OP’s son has already checked all the boxes for science / math courses (honors chem and honors bio with strong grades, AP Physics C with 5, AP Calc BC with 5). For senior year he will be taking post-AP math, and is considering which additional science course to take. The choice is between AP Chem and a higher level post-AP physics class. Between these two options, I am not sure why you feel that AP Chem would be perceived as higher rigor or more impressive.
It would seem to me that there could be possible benefits to either path from an admissions perspective… AP Chem might be seen as broader but also more cookie-cutter, while post-AP Physics would be unusual depth in physics for HS. We see lots of students here on CC with course schedules that have post-AP depth in math and computer science, or engineering electives, but it’s not as common to see post-AP physics.
So, really up to the OP’s son what he thinks would benefit him more in college, IMHO.
It probably matters which physics classes OP is considering. Just being “post” his AP classes does not necessarily demonstrate rigor. I would feel the same way about engineering electives. Some of these classes are clearly at the high school level, whereas in theory, an AP class is at “college” level. If OP is taking a college class in optics, sure. If OP is taking a high school elective, maybe not.
Perhaps the guidance counselor needs to weigh in as well. We don’t want OP to be compared unfavorably to students from the same school, even subtly, in that letter.
ETA: it used to be that students applying to MIT from the school where I teach, were told that they could just take “two of the three” AP Bio/Chem/Physics. That is no longer the advice, per the guidance department, to be competitive.
It’s not about higher rigor or more impressive but rather about a lack of breadth. I am not and admissions officer as I said but I personally would favor the student who has AP Chemistry if I were looking purely at students who are looking to major in engineering because doing so indicates the student will likely be able to handle both chemistry and physics at the university level. Honors Chemistry doesn’t demonstrate this adequately in my view since it’s really an introductory level science course that freshmen and sophomore often have to take. Yes, in some schools it’s a hard course but in those schools the AP version would likely be even harder.
i think people are getting side-tracked by MIT and its requirements but MIT does not admit students by major. What do engineering programs that admit students into engineering recommend students take? I expect many would recommend Calculus, Honors Physics and Honors Chemistry at a minimum if they are available to the student though I could be mistaken. It’s not just math and physics. In which case I would expect they like seeing students demonstrate proficiency in all three subjects not just two of them. Would they accept a student who demonstrates only proficiency in math and physics? Yes sure not saying otherwise but again it’s like anything. They may only recommend at least 3 years of social science but the 4th doesn’t hurt.
Engineering programs that admit students by major are typically at state schools like UCB, UIUC, etc. These programs are selective, but are not as selective as tippy-tops like MIT, Caltech, Stanford, none of which admit by major.
And has the advice worked? Are students getting in at the rate which is predicted?
Seems like shallow advice. The folks who wrote “Applying Sideways” are now suddenly counting up AP’s like they’re chips at a casino?
It’s possible that at @fretfulmother’s school, the AP science courses are the highest level or most rigorous courses available in the sciences. So in that case, it might be a good idea for students to take as many of them as possible, not because of “racking up APs” but instead taking the highest rigor.
In a curriculum with other high level science courses available, the advice might be different.
Cornell and Columbia admit into engineering I believe. Also for engineering, the top public schools are often far better ranked than what many consider to be tippy top on this forum ie. someone referenced Brown and that it would not be considered tippy top with regard to engineering. Apart from the three you mention, most other tippy tops for engineering seem to be public schools ie. Georgia Tech, Berkeley etc.
Also note that Caltech lists students have to have Calculus, Physics and Chemistry and requires that students take all of them in their first year. A student who has taken all of them at the AP level in high school is likely to have better preparation than a student who has not. Same with MIT since all are required though at MIT a student can test out of them. Students do get credit for Intro Calc if they have a 5 on AP Calc BC as well as Physics 1 if they have 5’s on both Physics C courses. Do I think a lack of AP Chemistry would be a deciding factor? No. However, for engineering all else being equal, I would expect it would be preferable to have more breadth than depth to demonstrate they would be well prepared for university level work in all three core subjects.
These public schools are tippy top in engineering, but what I meant is that they are not tippy top in terms of admissions selectivity 
I doubt that either senior year option would limit an applicant in terms of admissions to the public universities.
(My kid attends UCB in engineering)
Asking follow-up questions of the original poster to gain situational knowledge of their school may be more effective than making blanket statements of what is necessary because that’s how one HS does it
Hey folks, let’s get back on topic and avoid back and forth please.
I don’t think lack of AP chem by itself is going to hold this kid back from engineering admissions. He has lots of other STEM rigor, and a whopping 14 AP classes, including physics C and calc BC. I’m not sure about other schools, but Purdue admits tons of students to engineering who haven’t taken AP chem. He wants to dig into some higher level physics and math and that will actually stand out to admissions. I doubt anyone is going to care that he didn’t take AP chem.
In terms of “AP chemistry versus more advanced physics after AP physics C”, would the more advanced physics courses be at a college, and what topics would they cover?
For engineering majors, credit and advanced placement in physics is less predictable than for chemistry, because AP physics C may be less math-intensive (particularly E&M) and cover fewer topics than calculus-based introductory physics in college.
Most engineering majors at most colleges require the first two semesters of calculus-based introductory physics and one to two semesters of general chemistry (chemical and biomedical engineering majors have to take organic chemistry as well).
Even leaving aside chemical engineering, it’s more common in my experience looking at requirements for at least one semester of chem to be required rather than a third semester of physics.
I agree with the others who suggested taking more advanced Physics as opposed to AP Chem is not going to be an admissions issue (with a HS-level Chem class already on the transcript).
I also agree there is a better chance AP Chem will get you an advanced placement and/or usable credit. Although for placement purposes, if you look for colleges that use a Physics placement exam, that might be good. Credit is another matter, though.
But again, I personally would simply not worry about it for admissions purposes.
With the background you’ve shared about your son, he will get into the majority of the engineering schools where he applies—and maybe to all—without AP Chem.
Taking AP chemistry would still leave the student far behind those who did research with CRISPR in high school. But the latter is not the norm, and is not really relevant in most kinds of engineering anyway.
Taking college level O chem and doing CRISPR research in high school? As a household with chem and bio professsor parents, I can assure you that would be exceedingly rare. With the logic that the kid should prepare to be in a super elite position running NASA missions or teaching at a T5, what is actually enough in high school? Sounds like a recipe for poor mental health to me. The kid is doing what he likes and digging deep into his natural interests, which is healthy and something that admissions offices like to see. And is also simultaneously checking the boxes that must be checked to have a chance at elite schools. He doesn’t need to be doing literal gene editing in high school.