I have a 2008 Soma Double Cross DC Cyclocross bike. The bike has more than 8000 miles on it, but still looks and performs well. It's made with True Temper Prestige and the fit and ride comfort is an A+. The Frame size is a 60cm, I'm a healthy 210 lbs and use the bike for Century rides.
My only dissatisfaction with the bike is the strength and stiffness of the chainstays. I get a lot of flex in the BB area. The chainstays are really collapsed to make room for up to 700x42 MTB tires and a triple road crankset. I'll never use any tire larger than 700x32 and run 700x25 most of the time.
Would it be mistakes to have a good framebuilder replace the chainstays with something stronger?
Replacing both chainstays is not terribly difficult but will not necessarily solve the problem you have. The downtube contributes a great deal to BB "stiffness" as well, and you could end up spending a pile of money and not getting significant improvement.
Depending on how much you intend to spend, you may be better served talking to the framebuilder about a custom frame that addresses your concerns, or simply finding an "off the peg" frame that rides better than your present frame.