[Nexus 6 Themes and Apps] guitardedhero:
I began by responding to you and it turned into this, while I'm still standing here in front of the oven overcooking my buffalo wings. This is certainly not directed at you, rather, it turned into a preaching to the choir post.

That's odd, I remeber a 6p user getting it working on Chroma I think. I haven't tested on the legacy SuperSU 2.56 and lower but I'm sure it works fine as this thread would.likely double in size from the reports. Something is lingering, incompatible, or not being written properly.

First thing to always do is check /system for available free space. This was not ever really an issue before Marshmallow, but Android's latest OS in its full stock flavor simply crams the /system partition. From now on, until the /system used/free ratio returns to a manageable value, we all need get into the habit of checking /system space after every OS or rom install.

Second is to install/update BusyBox, pereferbly Stericson's Pro version since I use Pro's default Smart Install settings. Free version: https://play.google.com/store/apps/details?id=stericson.busybox

Third is to use Root Explorer, the only file manager I've used and one of the first apps I ever installed when I got my first android phone the Galaxy Nexus. Ever since, and still consistently, I see all kinds of reports of errors when managing through other file managers that I never see in my above-average usage of a file manager. For obvious reasons, the paid version is preferred, linked here: https://play.google.com/store/apps/details?id=com.speedsoftware.rootexplorer

Fourth, I would go ahead and dive into the systemless SuperSU so when it's mainstream rather than the legacy one you will already be familiar with all the failures, conflicts, and tendencies.

The surest way to a successful system mod is to start with a fresh /system partition. I can't remember the last time I used TWRP to backup or restore my phone, keep in mind that nothing of value is stored except for the nerdy zip stuff. I hated the long process and the major hit in storage space that I quickly learned the same result is achieved, assuming /data is your concern, by simply wiping system in TWRP and flashing a compatible rom zip. It is so quick, as it is not a Factory Reset, and takes up zero space as the rom zip is already there anyway. All data is intact and you have a fresh /system partition to play with. The only things missed will be the system modifications made before the dirty flash, which takes less time than restoring from TWRP or a Factory Reset.

Remember to always go into Mount on TWRP's home page to uncheck System after wiping it as TWRP mounts /system to wipe it but leaves it mounted. Some zips and rom's only toggle /system mount so the first event to occur during the flash is unmounting of /system which leaves it untouched throughout the flash. Very rarely, does having /system unmounted before flashing cause issues. If you find that /system folders/files did not write after flashing, then try mounting system in TWRP first. Remember, TWRP defaults to mounting /data and /cache and only mounts system when told to do so, which is what most of the scripts when written.

Always be observing of letter casing, permissions, and other patterns within the OS. Typically /system folders work best when set to 0755 and /system files when set to 0644. The few file permissions settings that work best at 0755 are your script and bin files in these folders for example: /system/su.d, system/addon.d, system/xbin, /system/etc/init.d...

Finally, don't worry so much about repeated failures, missteps, mistakes, and other unsuccessful aspirations as these actions are ultimately what grows our knowledge. If I put something together and it never had a single failure, frankly, I wouldn't be able to tell you why it even works.