A second bathroom increases the resale value of the home if say, it's on a different floor and presents some sort of convenience.
Think of your unhappiness with the two small bathrooms... a future buyer will likely feel the same way. Luxury is in and a big bathroom is a sronger selling point than two cramped back to back ones. Plus, you have your own comfort to think about...
If the main waste-vent stack isn't in the common wall (it's a HUGE great vertical pipe), it shouldn't be too hard to move the mechanicals. If it is, it's still doable, but you'll have to find a pro. Er, I'm not to sure about ductwork movability.