On Chrome and Firefox, at least, as long as I delete Array.prototype.whatever first, I get an enumerable property when I polyfill it.

Not saying that's the ideal solution, and there are certainly other issues with extending built-ins and clobbering the original name. The Chrome blog also mentions forcing a patch to legacy websites is an unacceptable solution (though I'm not sure I agree with that unless we want to maintain name compatibility with every library forevermore).

However, it's certainly not a matter where MooTools would have to completely rework what they're doing, or where the browser would have to make the property enumerable from the start.

In fact, it'd be easy enough to use a compatability shim on the site side that'd nuke all the conflicting properties from Array.prototype before Mootools ever loads, if they know they're on ES5 and would never use the native ones.

    > Array.prototype.map = () => { console.log('map, yo'); }
    function Array.prototype.map()
    > [].map()
    map, yo
    undefined
    > for (k in []) console.log(k)
    undefined
    > delete Array.prototype.map
    true
    > Array.prototype.map = () => { console.log('map, yo'); }
    function Array.prototype.map()
    > [].map()
    map, yo
    undefined
    > for (k in []) console.log(k)
    map
    undefined