Why would you include ES5 shims instead of using code that's well tested, already written, and bundled in a neat package.
I'm not sure how much you really need to test an each() loop. It is a very simple thing as are most of the other features introduced in ES5 that can be shimmed. jQuery doesn't include many of these new features, and I disagree with you that you should just omit them from your code because your DOM library, of all things, doesn't include them.
All the ES5 shims do is implement these functions exactly to the standard, and doing so is a very simple thing. Further, the code in a shim is only run in old versions of IE: New IE, and pretty much all running versions of non-IE browsers, implement these functions in native code (which obviously is much faster). jQuery does not defer to Array.prototype.forEach if it is available.
jQuery is the de-facto DOM library
No, it really isn't. There's a huge distance to travel from being the most popular to being "de-facto."
Hmmm, seems like a huge distance to travel from being 'I think ES5 shims are awesome' to a 'best-practice' these days. I'd be hesitant to use the kriskowal library in production, especially since it states 'This package requires quite a bit more attention and testing. It is not likely to behave as advertised in a large cross-section of browsers.'
There is no de facto DOM library. I just said as much ... jQuery would be "de facto" if projects adopted it without a second thought, and in my experience this doesn't happen except with beginners.
These 'beginners' are building working sites left and right every day. They don't need to feel they are on the bleeding edge of html, they just want their stuff to work reliably with a reasonable cost. Most of them don't write blogs, don't have githubs, don't own node packages. They develop web sites the same way that you and I drive our cars. They adopt jQuery without a second thought, and why shouldn't they?
jQuery is the de-facto DOM library (whether it should be or not), failure to see this is ignorance.