<p>At the top of the list are Harvey Mudd and Cooper Union. Both have a size and atmosphere similar to Caltech's; they aim for intensity at a similar level. Harvey Mudd in particular seems really, really perfect given what you say you are looking for. They have a really excellent physics program with high standards and demanding courses, and the undergraduate life is not a bad replica of Caltech's from what I gather. Cooper Union is similar and gives a LOT of merit money. Rose-Hullman also shows up regularly on lists of good physics/engineering schools. So look into those three schools, especially Harvey Mudd. </p>
<p>Now for some unsolicited advice (in the second person as if I were talking to your son). Ignore this ensuing paragraphs if you are uninterested in my unsolicited advice ;-) which is this: don't count yourself out of the Caltech/MIT game completely. Yes, the three factors you mention are an issue, but, on the positive side, this situation gives you a chance to really take risks and give it all you've got on the rest of the application. (I assume you'll be applying to Caltech/MIT as your first choice reaches.) Since, realistically, the only hope is to win someone's heart, the advice I would give is: try to write something really beautiful and insightful for the essays (easier said than done, I know). Talk about why you love science and what you would bring to Caltech. But the key is that the quality of the output should not resemble that of a high school assignment ("I love science because... I would bring to Caltech enthusiasm and a strong sense of personal responsibility..."). The bar is somewhat higher than that. Since in all writing, the key is to think about the audience and the goal, it helps to remember that here your audience is a Caltech admissions officer, a Caltech professor, and a Caltech student (the three people who will read your application) and the goal is to knock them over. That's not that easy, but you're helped by the fact that many applicants (often, numerically the strongest applicants) phone it in and submit something formulaic, docile, and typical. </p>
<p>So try to imagine that your job is to write really incredibly well (I always think of the fictional speechwriters Sam and Toby on the West Wing ;-) and try to write what they would write if you hired them. Imagine that you're composing a symphony, a delicate and perfectly constructed kind of work. Aim to get your audience on their feet applauding at the end. There are a lot of good guides on writing, and you should read them for technical guidance... but my feeling is really that a major component of how good the product will be is how seriously you approach the endeavor. From the essays I've read, it's pretty clear to me that most people dash off something in an hour or two. They either aren't aiming to impress or don't realize how hard it is to produce an inspiring (as opposed to insipid) piece of writing. Once you avoid those mistakes, and set about doing this for real, the only remaining ingredient is courage. It is no surprise that one sees lots of very similar essays because almost everyone is doing the same boring, cautious dance -- trying not to say anything that could be seen in the wrong light while saying all the right things. If you shed a little of that caution and talk more honestly, that honesty will be appreciated. There are few things more beautiful than a real human voice breaking out of the page, and I'm personally willing to ignore a lot of flaws in someone who has enough courage to produce that kind of essay.</p>
<p>My feeling from my conversations with the other Ben at MIT is that especially with our friends in the east, that sort of thing can make a lot of difference and can go a long way toward remedying other deficiencies. At Caltech, we're a little more rigorous on the numbers side (or so it has seemed to many people, apparently) but my guess is that a lot of people on the committee would be willing to go to the mat for someone who won them over despite the lack of traditional strengths. I know I would.</p>
<p>I realize that your question was about other schools to consider. And they're very important to think about. But I'd take this situation as a challenge. I think it can be done, if it's truly your dream to come here. (That isn't just babble. I wouldn't say the same if your stats were a little different.) With the right sort of approach, it is possible -- somewhere in the Platonic realm of yet unfinished things, there floats the application that'll get you into your dream school. Now try to produce it. Good luck.</p>