"The way I want handwriting recognition to work is to take notes by jotting them down inside an app like OneNote, and have Windows recognize that automatically, behind the scenes, optionally without replacing my handwritten notes with printed text. Then, I want to be able to search my handwritten notes using full-text search."
OneNote actually already does this! Try searching in OneNote for things you've written in pen and it will show those notes.
I don't believe the OneNote Metro app supports indexing handwritten notes.
If you open the same notebook in the Win32 client and allow it to index and sync back to Sky/One/WhateverIt'sCalledThisWeekDrive you should be able to search through previously handwritten and Win32-client-OCRd notes in the Metro app.
You need the full version of OneNote for the recognition.
It's vastly superior, but on the plus side, if you're using OneDrive or Office 365, you can edit existing notes either one depending on your needs for a given situation.
OneNote actually already does this! Try searching in OneNote for things you've written in pen and it will show those notes.