The animation when you go from the lock screen to the home screen is stupid and a waste of time.
Also, the new folders layout is actually hurting the ergonomics of the phone. On the iPod touch/iPhone where you had 10-16 apps in a folder under iOS 6 now requires 2 pages in the folder instead of one on iOS 7. For the iPad, it's even worse, a full folder on iOS 6 (20 apps) now take 3 pages withing a folder on iOS 7.
it actually helps the ergonomics of the phone if you look at it from a logistical standpoint.
the old method would take an icon with three apps in a row and turn it into a spread of 4 icons in a row. if you wanted to go to the fourth app in a folder, in the icon it would be the first app in the second row, and once the folder would open, it would be in the exact opposite place: the last app in the first row.
this was very anti-intuitive, would lead to user lag unless you were fully used to the system moving icons around like that.
now that the folders match the contents of the folder icon, things are a lot more fluid, it's quicker to go from clicking the folder to clicking the icon you want, because you can already visually see exactly where it is. in this way it's more ergonomic.
for people with dozens of apps in a folder, while it throws a bunch of apps to the next page, there is no longer such a low limit on the amount of apps you can have in one folder. not sure about you, but i hated having multiple folders devoted to the same category of apps. another problem which has been solved in an ergonomic way.