For the first time, an iOS upgrade is leaving a bad taste in consumers’ mouths. While it’s usually the case that upgrades are viewed as improving the iPhone experience, a new survey finds iOS 6 actually hurt Apple’s sterling customer service reputation. Apple’s decision to replace Google Maps with its own service appears to be the root cause, say researchers.

“We have always seen an increase in device satisfaction as consumers upgrade their mobile operating system from one version to another,” On Device DEO Alistair Hill told TechCrunch. While the rating for the upgrade from iOS 4 to iOS 5 received high marks, the move to iOS 6 saw ratings decrease to 7.65 from 7.75. On Device surveyed nearly 16,000 U.S. iPhone owners…

Apple’s mapping efforts have come in for much criticism because they provide fewer details than Google’s service. Apple last week responded to the criticism, saying the mapping would improve as more people use the new feature. However, some aren’t waiting for Apple Maps to get better and are seeking alternatives. Japanese smartphone users are flocking to mapping veteran Navitime, reports the New York Times. Meanwhile, Google chairman Eric Schmidt speaking in Tokyo and doing all he could to not say ‘I told you so,’ said “It would have been better if they [Apple] kept our maps. But what do I know?”

The Cupertino, Calif. company seems to have gotten the message. Recently, the company began increasing its mapping staff, including modelers and 3D image experts to improve widely-maligned images.

Ironically, Apple’s Maps, along with AssistiveTouch and Zoom features are being lauded by visually-impaired users employing the iOS VoiceOver system to read text aloud. However, Apple was given lower marks for its updated iOS App Store layout which offers a new horizontal arrangement for top apps, books and music. According to AppleInsider, the refreshed App Store appearance plays havoc with VoiceOver. App ratings can no longer be read to visually-impaired iPhone owners, a reader complained.

The survey and comments follow Apple’s wide lead in a J.D. Power customer satisfaction survey, showing the iPhone maker outdistancing other smartphone makers, including those powered by Google’s Android.

Apple is likely correct when it said last week that its cloud-based Mapping application will improve as it is used by more and more people. While the company needs to beef up its mapping experience to stem the tide of bad PR from maps that put buildings in the middle of the ocean or omit landmarks, we are less than a week into its wide distribution. As for the problems experienced by visually-impaired users, the company has shown great sensitivity to their needs in the past, quickly offering updates to troublesome software, and I don’t see that trend changing with iOS 6. Ultimately, iOS 6 will gain more converts than critics.

What do you think? Were you disappointed by iOS 6? What’s your favorite iOS 6 upgrade story?