Although I'm not in agreement with flushing every year which IMHO is overkill, it is something that should be done periodically, depending on mileage and time. Your dealer may be a little overenthusiastic but he is not out of line. As mentioned, if your fluid is dark brown it has a lot of moisture in it. Moisture is what makes it turn color.
Stainless steel lines are a little pricey but well worth it. Along with longer life, you also get a little better braking power because SS lines do not expand like rubber ones do...