First off, riding in the rain isn't that bad once you get or make a cheap rain suit. They're only like $20 for a "frogg toggs" which is what I use. As for the milk crate, try spray-painting it a little just to give it some happiness. It's definitely a nice thing to have while riding. You can haul all kinds of things. Of course, a backpack will work but may get your back all sweaty.

I just use bungee cords for the crate and it works great.