Google needs a better cloud-based backup/restore solution. Sure, they've been improving things, such as having app DATA backups to go with their "we'll load your apps back for you" feature... many (if not most) times, it's the app data we want more than the app itself. But not all apps support the feature. The only way to keep that stuff handy is to load something like Titanium Backup.... but to the most out of that, you need a rooted device (and some of its features might get handcuffed come future versions of Android). You really should be able to wipe the phone then check off "Restore system and user data" when you restore the phone.
The 'stock' recovery typically means "FACTORY RESET! Do not pass GO!" for most people. For the more tech-aware folks, what is one of the first things that gets loaded on a phone? Even those not looking to root their phone or load a custom rom typically load a custom recovery..... why do we even need to have custom recoveries like TWRP and CWM? All those features should be available right from the get-go.
I guess, at least, from what I've seen, Google recognizes this and is working to resolve it. As I mentioned earlier, they are implementing app data cloud backups, they've been leveraging Google Drive for backing up photos and videos.... hopefully this is just the start.