Essentially, every single GNU package on a Linux system has a reasonable non-GNU alternative. The Linux kernel, on the other hand, doesn't exactly have a simple drop-in replacement. Moreover, it's obvious that the kernel is the most sophisticated and non-commodity software part because the GNU people never managed to deliver a working kernel.
As such, it's probably better to consider the system Linux with a little bit of GNU thrown in if you want it. And if you count android or embedded systems, a lot of Linux systems actually have absolutely no GNU software whatsoever.
Free software is good, but RMS has been a pretty terrible advocate for it. His unwelcoming, aggressive, and pedantic behavior has really hamstring GNU tools. It's no surprise to me that GNU software is being phased out (see: GCC, bash) by developers and that the GPL has largely failed as a license.
Why do you think the kernel is harder to replace than coreutils and libc? There have been working replacements (ex. Debian/kFreeBSD), and in many systems replacing libc/coreutils is effectively impossible (having once tried this, I can tell you that swapping coreutils with busybox on Debian results in a sort of working system, but completely breaks package management, IIRC).
2. That said, I also disagree that the BSD kernels are inferior. Linux is catching up to FreeBSD's network performance, but it is playing catch up. NetBSD, AFAIK, blows Linux out of the water in terms of hardware support, although it is behind on newer stuff. As to kernel interfaces, of course they're different, but I'm not convinced that that's bad. (ex. I've not used kqueue, but I'm told that it's far better than the Linux equivalent.) Now all that said, I'm happy to grant that Linux is certainly benefiting from the sheer number of devs they've got, and is a good all-arounder; less secure than OpenBSD, less portable than NetBSD, less performant than DragonFly BSD, but secure enough, portable to most hardware in wide use, and performant enough for most users. But it's not universally superior.
In fact DragonflyBSD is slower than FreeBSD in most benchmarks. I've always been under the impression that FreeBSD is for performance (though worse than Linux), OpenBSD is security and correctness (my favorite of the bunch), NetBSD is portability, and DragonflyBSD is for experimental crazy shit (my second favorite).
https://www.gnu.org/gnu/incorrect-quotation.en.html
>A quotation circulates on the Internet, attributed to me, but it wasn't written by me.
> The version with Linux, we call “GNU/Linux.” It is OK to call it “GNU” when you want to be really short, but it is better to call it “GNU/Linux” so as to give Torvalds some credit.
The above text is a fabricated quote wrongly attributed to RMS.