<p>I think Yale is the better choice here, for a few (hardly necessary ;)) reasons:</p>
<ol>
<li>The combination of the Perspectives in Science program (assuming you are accepted to the program, which, given your success so far, wouldn’t surprise me) with the combined BS/MS degree option gives you the opportunity for an even better program than Penn is offering, and you don’t have to lock yourself down to Penn for your second degree.</li>
<li>Yale is POURING money into Science Hill…$1 billion in new facilities.</li>
<li>Yale is a much better option for being well rounded. Yale is renowned for humanities in addition to being great in sciences.</li>
<li>As you said, Yale blows Penn away in terms of residential life, campus, etc.; this definitely makes up for whatever you think New Haven lacks in comparison to Philadelphia.</li>
<li>Yale is overall a better school than Penn. :p</li>
</ol>
<p>I do think it’s commendable that you’re giving this a lot of thought - most people would choose Yale’s name without giving much thought (if any) to the actual program. I still think you should pick Yale, but clearly, you should do so because you’ve thought everything through.</p>