A non-instrusive notification system would be my main request, but you won't see GPS/turn by turn maps on iOS as standard like Google provide on Android. Why? Because Apple sell TomTom, Navigon, and Co-Pilot Sat Nav apps for very good money on the App Store. For example, TomTom UK & Ireland is the third biggest grossing paid Navigation app on the UK store, costing £49.99.
Apple get 30% of every app sold, so for every copy of TomTom that's sold (in the UK), Apple take £14.99 ... so you can say cheerio to a free turn-by-turn maps/GPS app in iOS5 in my opinion.
I'd like to see a change to how the multi-tasking bar is opened. I know there's the multi-touch gestures you can activate if you Jailbreak, but surely the iPhone could have two finger gestures implemented in place of four fingers (like on iPad) due to the screen size (I don't want a bigger screen on the iPhone personally).
A third "feature"? How about properly optimised code that doesn't make the iPhone 4 run sluggish? In all seriousness though, WiFi syncing would be nice. Again, I know it's available if you jailbreak but costs $10.