Don't know if I'm doing something wrong with Android, or whether it's just because my phone is currently restricted to ICS, but I find the notification system appalling compared to iOS.
On iOS, I get a notification and (if I choose to make it appear there) it pops up as an alert on my lockscreen which then goes into a list of alerts since I last unlocked my phone. If any of them interest me, I swipe over it from the lockscreen and it takes me straight into that app.
With Android, I get nothing on my lock screen at all. What I do get, once I've unlocked my phone, is a little icon at the top telling me that the app wants to tell me something. I then have to pull the notification window down to see what it wants to tell me, at which point I can tap it to get into the app.
I have installed "iPhone Notifications" on my Android phone, which helps a little - at least I get a pop-up message on my lock screen - bit it's still some way behind what I'm used to on iOS.
Custom keyboards - thank god for that on Android. I found it almost impossible to type on the stock keyboard, whereas I've rarely had a problem with the iOS one.
As for settings, again I personally find iOS much clearer on this.
Everything is clearly not rosy in the iOS camp - I certainly miss widgets/live desktop when I'm using my iPhone for instance, but many of the other "issues" you list are subjective at best.