- How to deprecate a feature (I created http://drupal.org/node/1400346 to attempt to solve this, but admitedly, it's a very dangerous module) - Ever created a feature with tons of things in it? Hello, 5 minute load times for admin pages! - How do you merge two features together? How do you commit just one feature and not another (say, one you're still working on?)
The CMI initiative will hopefully take care of a lot of the messiness and bugs in Features.
I've merged features together and it was not as hard, at the end it is all code, you just need to be very careful, but at the same time you have git to revert if something goes wrong.
I don't understand the part about committing just one feature. You can commit just one =P.
I finished up a project earlier this year that has more than 300 modules active in a custom install profile, with 10MB of features modules stuck in there. We committed/contributed to a few fixes in core and Features to speed it up greatly. That's out in the wild on major sites and doing fine.
We didn't have any terrible admin screen issues, or indeed any terrible issues beyond occasional painful version control collisions.
Features and things like http://drupal.org/project/drush_make is what makes a lot of the drupal distributions (http://drupal.org/project/distributions) that keep popping up because sourced controlled, feature driven development is now possible in drupal.
Also the testing part has been improving, and although very few of the contrib modules have tests most of core has automatic testing in place for when you submit a patch as you can see in the issue queues (http://drupal.org/node/466576).