Yep... The wing root is indeed massive on the A380, and nearly all of the lower deck CW seats look at the wing, so if that is what you want, then upper deck is better.
In regards to the bathrooms too, if your partner can, try and use the bathroom at the front, on the left hand side of the staircase (as you look forward in the aircraft) as there is a seating bench in there too, so useful for getting changed, support for getting up and down and the likes. The bathrooms at the front are very spacious, so no problems moving around etc.