Besides wasting space, it also means the battery has to be a single monolithic entity, can't be too flat (or the case would use up the entire space the battery occupies), and can't have any components over it.
It's 6 different cells, that span the entire width of the laptop. They're glued in, and they use pretty much every bit of space they can. There's also a ribbon cable going over them, which I believe is the trackpad cable.
Why not putting these bag shaped battery cells in a plastic case? Couldn't this case still have any shape?