Larger windows and humidity will be possible due to use of composites, not because they will cost much more to develop. The reason aircraft now are not more humid is because moisture would condense of the cold fuselage and accelerate corrosion and metal fatigue (very expensive). That is why the airplane's environment must be constantly dried, so I imagine in the 787 more moisture from perspiring human bodies will be allowed to remain in the air. Composites do not suffer this problem of fatigue in relation to corrosion. Also, larger windows are possible only because a stronger composite structure allows for larger holes in the fuselage.

As far as LED lighting does... my guess is is actually cheaper, considering it weighs less, takes up less space, and possible makes customers happier? I doubt dimming windows is so expensive either... it if were no airlines would agree to have them. Maybe they are even cheaper because there no need for shades that take up weight, break etc.

The real cost of Concorde (as any aircraft) is not small, little frills but rather engine (in)efficiency, fuselage and wings costs. The rest is mere pennies... I think.