One of the main arguments against Google’s Android operating system is the fragmentation that is spread across hundreds of devices and various software versions. Apple has even taken shots at the OS, highlighting how within a year, almost all iPhones are running the latest system version, compared to about 7% of Android users on Ice Cream Sandwich. But with the introduction of iOS 6, which the Cupertino-based company claims will deliver more than 200 new features, Apple may finally have to deal with fragmentation as well.

While the iPhone 3GS and iPhone 4 will be compatible with iOS 6, both devices will get a version of the software that forgoes key features. As noted by Ars Technica, Apple’s impressive 3D Flyover feature and turn-by-turn voice navigation found within its new Maps app will only work on A5-powered devices, meaning the iPhone 4S, iPad 2 and the new iPad. To make matters worse, the iPhone 3GS doesn’t support FaceTime and it won’t be able to handle offline reading, shared Photo Streams, VIP lists or Flagged Smart mailboxes.

While the situation might not be as bad as many claim it is on Android, Apple will continue to face difficulties when attempting to keep its older hardware up-to-date.

Apple’s list of feature limitations is as follows:

Features are subject to change. Not all features are available on all devices. Some features may not be available in all countries or all areas. Flyover and turn-by-turn navigation will be available only on iPhone 4S and iPad 2 or later. Cellular data charges may apply. Siri will be available only on iPhone 4S and iPad (3rd generation) and requires Internet access. Siri may not be available in all languages or all areas, and features may vary by area. Cellular data charges may apply. Shared Photo Streams requires iOS 6 on iPhone 4 or later or iPad 2 or later, or a Mac computer with OS X Mountain Lion. An up-to-date browser is required for accessing shared photo streams on the web. FaceTime over a cellular network requires iPhone 4S or iPad (3rd generation) with cellular data capability. Carrier data charges may apply. FaceTime is not available in all countries. VIP list and VIP and Flagged smart mailboxes will be available on iPhone 4 or later and iPad 2 or later. Offline Reading List will be available on iPhone 4 or later and iPad 2 or later. Made for iPhone hearing aids require iPhone 4S. Find My Friends and Find My iPhone enable you to locate iOS devices only when they are on and connected to a registered Wi-Fi network or have an active data plan. Not available in all areas.