There are things that in my opinion are better on the Bavaria:
The Galley is bigger and probably more functional, the boat seems rock solid (look at that guy doing gyms on the handrails), plenty of handrails, that big swimming platform is a lot larger than the one from the 409, the boat has a geenaker retractable boom and the possibility of having 4 winches on the sides (German sheeting for the main sail). It has also a very smart way to protect the outside plotter from weather and thieves and off course it has that Kevlar protection on the hull against impacts.
On the Jeanneau 49:
The interior and the outside have a better overall design, the boat is faster, with more sail and less weight, the lateral passage on the deck is much bigger, the Genoa winches are closer to the wheel.