In fact, the standard initramfs *needs* a number of utilities in order to boot the system anyway. So put all the necessary booting/fixing progs in the initramfs, and put everything in /bin and /lib on the hard drive. Building with '--prefix=/' will handle most of it; the rest is in system-specific scripts and config files.
That said, I can still see a good reason to keep /usr separate. Keep the most commonly used utilities, programs and libs in / and put the rest in /usr: it may well make it easier to keep /bin, /sbin and /lib dirs cached (the dirs, not necessarily their contents). The less you have to hit the disk, the faster the system will be.
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