Ads: The homescreen has a couple of small store links at the bottom that are relatively unobtrusive. There are no recommendations forced on you unless you go to the store. There is a store button at the bottom of the homescreen, which I imagine is pretty handy if you actually want to get your eBooks from them.
Organization: You have to set up book categories after putting files on the device (like how the Kindle 3 was back in the day) but there are no forced labels or anything. There are at least 2 homebrew launchers that replace the homescreen, one of which lets you use a directory structure for files.
There is no screensaver advertising at all, unlike the Kindle—you can set it to display the cover of the last book you read, a generic "sleeping" message, or upload your own pictures for random display. I was really surprised by this; it's like they asked Kindle modders what they wanted and just made it the default.
There is a trick for skipping user registration during the onboarding experience by plugging the device into a PC and editing a YAML file, allowing you to use the device without giving them any info at all—unthinkable on Kindle!
Rakuten is a small Canadian company, so their niche is being less shitty than Amazon. If they ever stopped doing that they wouldn't have any customers.