The Important Thing, of course, is to divide a system into modules in the Right Way. The Natural Way. You want the parts to seem like they're the obvious parts doing the obvious jobs. But getting it to break down that way is an art.
There's a Taoist metaphor of two butchers. The one hacks and hacks and works hard at chopping the carcass into the parts he's trying to separate. The Taoist butcher, though, is somehow in tune with the thing and effortlessly hits it
right at the places it wants to split anyway, and bloop, it falls apart. See CookDing
If you don't work at getting natural divisions, you'll get ugly unnatural ones. So the natural way is in a sense less natural. And yet, once you find them, the natural divisions are really there and really more natural.
I suppose the kind of "natural" you find when you keep on going past unnatural is returnatural. I should submit it to that NPR words contest.
The Tao of the butcher is to sharpen your damn knife. That is not enough, hacking with it will quickly make it dull again. And if you make it too sharp, it will break when you hack