Very different places. Here are some factors to consider:
Middlesex is a lovely campus within a small town, access to Boston is about 30-40 minutes.
They have lots of strong athletes.
They are academically rigorous.
Milton: More urban though I can’t really say I know the vibe. We didn’t look at it. I’ve driven by it. Close to Boston.
The 50/50 Boarders to Day will change things IMO.
They let kids in middle school so there will be an established group of kids who know one another.
I’d check the number of international students.
I’d check the academic rigor more. Don’t know enough about it.
For both, I’d check STEM programs in terms of:
Do they have advanced STEM classes esp in unusual subjects?
Are you going to be a kid who runs out of Math? If so, check to see how classes beyond Calc BC run ( and if they run every year).
Do either have a STEM center? I don’t remember Middlesex having one. We’re a STEM family, when my kid looked 4 years ago. It was very solid in STEM but not outstanding. Had classes but no internships and nothing that stood out in this dept. Might have changed.
College matriculation doesn’t really matter as you might do better or worse than others. No one really knows who is accepted and why.
Both seem like good choices. I think I’d lean to Middlesex but it’s not possible to determine which is a better fit for you as we don’t know what you are looking for in a school.