I think that when you evaluate a bike you have to assess it as a whole.
I think that the most important thing is fit. Smaller bikes are smaller all over. If you start with the premise that you have to have 29" wheels, you are going to have to make some comprises in top tube length, head tube angle or toe clip overlap for the larger wheels to fit.
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My greatest fear is all of my kids standing around my coffin and talking about "how sensible" dad was.