While Apple may have the majority of its customers using the latest version of iOS, every new software update typically breaks compatibility with a round of older devices. iOS 6 is no exception — we've already learned that the original iPad and third-generation iPod touch wouldn't receive the update at all, but even devices receiving iOS 6 will miss out on some key features. Most notably, only A5 or A5x devices (the iPhone 4S, iPad 2, and new iPad) will get to use the new Flyover and turn-by-turn navigation features in iOS 6. Apple doesn't give a reason for this, so we can't say for sure that the older processor in other iOS devices is the limiting factor here, though it's certainly something all the eligible devices have in common. The iPhone 4 also won't be able to take advantage of Facetime over cellular networks, with the phone's A4 processor again potentially being the limiting factor there.
The iPhone 3GS in particular will be missing out on a number of other features — shared Photo Streams, VIP and flagged email features, and the offline reading list will all be missing in action on the iPhone 3GS. Given that the iPhone 3GS is just about three years old, we can't say we're surprised to see some features not making it over, but it's still a bit of a bummer for those who may have picked it up for free on AT&T recently.