[sjs]

It doesn't necessarily double the number of flags, it doubles the number of boolean flags. And if you use a convention like joeyh mentioned then the length of your help text won't double, nor will the cognitive burden on users who have to remember the options.

A disadvantage of this system is that --no-x might not always make sense or read well so if you make it consistent it may be weird. On the other hand if you use --no-this and --without-that then you are increasing the documentation and cognitive burden on yourself and your users. For most geeks this is admittedly a pretty minor disadvantage but it's the only one I have off the top of my head.