I'd suggest Yocto is the de facto standard for this kind of embedded device. It's a bit complex behind the scenes but general building and updating packages is fairly straightforward.

Bringing up the edison is very easy. The bootloader supports DFU, so you can simply connect USB, reset, and flash the system images.

If you're coming at it from a higher level, it has a node.js and ssh services running by default, so it's easy to start tinkering.

There's nothing with wrong with yocto itself, it's a build system which allows to create a custom Linux distribution.

It's the way Intel dealt with whole thing, that makes me cringe. It's poorly organized and unaccustomed to any serious changes.

Yocto is a bit like gentoo for exotic architectures. It allows you to create your distribution by cross compiling everything from source, and applying multi layered patches. It is a buildroot with steroids.