It's difficult for me to comment on this excellent question, but I think it has to do with prosecutorial discretion. It's difficult to interfere with that exercise of discretion.
That being said, should the prosecution have laid a hundred thousand charges? No, absolutely not. That would have been unmanageable. The only choice was to lump them together in some way.
Could more charges have been laid? Yes. Could fewer charges have been laid? Yes. This is probably part of the agreement that was negotiated. However, I don't know, because I wasn't there.