Wow. I find myself disliking almost everything about the 1.6 update. Think I'll be reverting to the prior version (thank you Time Machine). Ok, being able to easily read the whole of long clues is a good thing, but for everything else...
I can no longer see what errors I made in the process of solving a puzzle. Used to be that I could tell the difference between a letter that I got right on my own versus one that I initially got wrong, but corrected after checking. I'd tell my wife "two greens on the LA Times today" (or no greens if it was a good day for me) the green checkmarks being letters that I corrected after the initial check showed they were wrong. Now there appears to be no way to distinguish. Once I correct the error, there is no way to tell that there was previously one there. That alone is huge and enough reason for me to revert.
Maybe you could use the "revealed" color for that. After all, correcting a letter after having been told that I got it wrong is pretty much like doing a reveal, even if I didn't actually use the reveal button (which I never do). *PLEASE*. Or anyway something so that I can tell. That's sort of a daily friendly competition between me and my wife - to see who got the fewest "greens" on today's puzzle.
Speaking of reverting, I despise auto-save in general. That's one reason I have not updated to OS X 10.9 (and probably won't ever do so). And Black Ink 1.6 seems to have no way to quite without saving. The closest thing looks to be to revert to some prior save. I don't want to revert. I just plain want to quit without littering my disk with old saves of puzzles from months ago.
Took me a while to find how to reopen a puzzle as unsolved so that my wife could try the same one. I used to just not save it (see above). Eventually did find it in the edit menu, though it seems to be a good way to get the app to crash (crash report sent).
I suppose the crashes are at least likely to get fixed. But the rest seem like intentional changes in a direction I consider to be for the worse.