I may be too late to help with your decision, but I'm embarking on the three-year JD/MBA at Wharton/Penn this fall and would be happy to lend some insight. PM me if you have any specific questions.
The value of the JD for someone who wants to return to the business field after graduation is a very contentious topic. Short answer is that it depends greatly on what you want to do with the degree and only if you can confidently pronounce in absolute terms the benefits you'll derive from the degree. Personally, I wouldn't even have considered the dual program if it weren't for Penn's shortened timeframe. For me, a JD will be very helpful but certainly not vital. For that reason alone I didn't apply to HLS.
But if you have the funds, the patience, and the need, I don't think you can top the "wow" factor of a Harvard JD/MBA.
But in my opinion you're absolutely correct about the relative strengths of HBS and Wharton. Whereas HBS exposes all students pretty much the same, theory-based curriculum, Wharton to a much greater extent allows students to customize their programs of study and, thanks to Wharton's size and the sheer breadth of its offerings, take classes in very specific, almost arcane topics. I'm a real estate guy, and the value of that flexibility is unquestionable. I'll get a much better real estate education at Wharton than I would have at HBS.