1) The greatest challenge for Tracking Protection seems to me to be not technical, but strategic: How do you protect users from tracking without creating a backlash from the tracking industry and their customers (the whole Internet economy built on tracking) that will make the outcome worse or no better, and after an expensive battle. As an extreme example, if the next release of Firefox cut off tracking for all its users then I think there would be a war, including possibly lawsuits and an arms race between trackers and tracking protection. The users would be no better off (or worse off) and it would consume Mozilla's resources.
2) How do they plan to protect the great majority of users who lack the knowledge and skill to understand tracking protection? Remember that most users barely know they are being tracked, much less what that means or how it's done. Many users I deal with don't know the URL field from the search box on their home page; they don't understand what a web browser, web page, or remote server are, much less their components, requests, JavaScript, etc. They lack even the framework to begin understanding tracking. Most other end users I know would be overwhelmed by the concept and extra hassle to load a page. Also, how will most users understand why the webpage is malfunctioning, of all the possible reasons, and what to do about it? Maybe they'll think Firefox is simply broken. Maybe this is why Tracking Protection is available only in Private Browsing right now, and hidden behind a small, somewhat obscure icon (if I understand correctly); maybe that's a way of limiting it to more technically skilled users. Providing tracking protection to technical users has been done, via Ghostery, Disconnect, etc. I'd like to see it become available to everyone else. (That's not a criticism of Mozilla - this is a great, precedent-setting step forward, establishing that major browser vendors might block tracking and act in user interests over industry's, and hopefully creating some competition in that area.)
Maybe the first step is to raise awareness of tracking and the idea that users benefit from and should have the option for privacy, which can be done by simply telling users about Tracking Protection when they open Firefox after the update, whether or not they actually use it.