I've had android devices since the HTC Magic (Feb 2009) and I have to admit I was a Android Fanboy.
Roll forward 3 years and many android devices later I ended up with an iPhone 4S because I got it for free & it was the best device I owned at the time (replacing a Xperia Mini Pro I was using as a backup phone).
I don't mind the iPhone but there are plenty of niggles that I've had to jailbreak to save me a lot of headaches...
Default Apps - I use Chrome (cross platform bookmarks, history, passwords and 'whats open on other devices) and Google Maps is just better... It was driving me nuts that iOS demands I use Safari & Apple maps.
Folder Sizes / No app draw / forced icons - These go hand in hand, without an app draw and my hate for icons all over the place I like having a single page (or maybe 2) with folders etc. How annoying is it having a folder called Games and then later down the line having to make a 2nd one called games or have something like "Quick Games" and "RPG Games" etc.
Quick Settings / Widgets - Again, being able to quickly turn on / off wifi, bluetooth, 3g without having to go though multiple menus.
Wifi off when screen off - I now understand why so many iPhone users claim so much more battery life, its because the wifi isn't persistent. Turn the screen off and few seconds later wifi turns off... well that wasn't much use when I didn't have a sim in my iPhone for 4 months in Canada.
So now I can understand why people do like the iPhone, its pretty, fast and sleek with more polished apps however it just doesn't offer the system and UI customisations to please me on a device I spend the majority of my time using.
HTC One inc next month and the iPhone 4S will be wiped, reset and given to my tech illiterate Father who will make the most of it without noticing its flaws.