Why get rid of checkboxes?
Checkboxes are one of those interface elements that cause a lot of usability issues. Due to their size it is difficult for a lot of people to actually tick a checkbox - even with a mouse. Some browsers make the label of the checkbox clickable as well which makes it slightly easier to use. But once you try using your thumb (or other fingers) on a touch interface it will probably take a few attempts until you actually manage to hit it.
Design wise checkboxes are a little annoying too because the operating system has complete control over the looks of the checkbox.
The solution is to replace checkboxes with something that's more user friendly, works on all devices and can be designed in a consistent way. There are many java script based solutions out there but we've decided to go for the "itoggle" project.
It's a simple seven sub-theme that replaces all checkboxes with itoggles. Using our code you can also implement it with any other theme out there (we use a fork of the rubik theme).
The script relies on a special browser behavior (click events being passed from the label to the checkbox) and should work fine in most modern browsers. But we definitely still got some cross-browser testing to do.
Have fun toggling!