1. Cramped App Store:
Although the Apple App Store's makeover is an improvement in aesthetics, search results are limited to one at a time via the iPhone, so you have to do a lot more scrolling. In theory, it's smart to highlight quality over quantity, but it doesn't always hit the mark. Plus, the layout is a bit cramped.
2. Maps Apps
Apple's new Maps app has been perhaps the most discussed and most griped about new feature on iOS 6 so far. In addition to the app omitting transit directions, users discovered that mapping imagery included a confusing cluster of broken roads, misplaced clouds and national monuments all out of whack.
3. YouTube App
Although everyone has been buzzing about the missing the Google Maps app, the Google-owned YouTube app is gone too. However, unlike Google Maps, a new (superior) version is downloadable via the Apple App Store.
4. Too Much Facebook
When Apple opened up social integration to Facebook, which will be key for allowing users to share pictures and post status updates without having to log into the app, it also merged your Facebook contacts and calendar automatically. The good news is that it's possible to turn off the default function if you feel overwhelmed with information.
5. Inconsistent Fonts
The Find My iPhone feature includes a font we haven't seen on iOS before, and it's inconsistency with the rest of the software has some perplexed.
6. Inconsistent Colors
Although some seem to love the color changes made to certain built-in apps, others are bothered that the new schemes aren't consistent throughout the interface. For example, the main coloring for the phone app went from black to silver, while the camera app went from silver to black.
7. Constant Alerts
iOS 6 has introduced a slew of new features to keep you on top of meetings, birthdays and events, but it also loves to remind you over and over (and over) again when things are coming up or there is a change to iCloud calendars you're subscribed to.
8. Buggy Calendar
Tapping "Today" button in the Calendar app can cause it to become skittish for some users. In fact, it can sometimes scroll mysteriously moving all by itself. Gremlins or just a bug?
(Reposted from Mashable)