Apple is still a bit behind when it comes to software updates: they’re all done through iTunes, even minor updates, like the recent 4.3.3 and 4.2.8 which brings a fix for location caching. Beyond iOS 5, though, we will start seeing over the air (OTA) updates for iPhones on Verizon, according to 9to5mac. The only downside to this is data loss in the event that the update doesn’t work; currently, you’re forced to back up your iOS device’s data before processing an update. Doing an OTA update wouldn’t provide you with this luxury.
It’s unlikely that we’ll see Apple go with OTA updates for full operating system upgrades, since those can clock in at near 500MB, and certainly the carriers don’t want their networks to be hampered with these massive downloads. The updates could be pushed while over WiFi, but again, because the iOS updates tend to be so large, it could take several days to download over WiFi if a user is seldom near a hotspot.