Lark Knight wrote:
To date the Masterworks I have with the new spine design are Thor Vol. 11, Cap Vol. 6, and Avengers Vol. 12. However, I still haven't had the heart to shelve them with the rest of my Masterworks yet. Anyone else having this problem?

It's really not as bad as it seems.  I have mine all added to the end of each respective title's run, followed by the next title's old-style spine, and it hardly makes a difference.