I just use a big duffle bag that I got as a freebie at an old job.

It has separate zippered compartments at either end, and one of those is mesh, so I keep the shoes in there. There's a separate little pocket to hold a water bottle and I keep a container of chain lube in it. The big compartment in the middle holds the helmet and everything else. I put small things in a separate plastic bag so they don't get lost inside the big compartment.