Same as many others:
1. Quality
2. Service and warranty. Just take it to the Apple store.
3. Software is always updated.
4. Can't remember the last time I had Safari crash. Last Windows laptop I owned around 2007, IE explorer crashed more times then I could count, often times several per day.
5. Resale value. Last December, I sold my unlocked 16GB 4S for $350.
Tried to sell my at the time, 6 month old Nexus 4 and got offers lower than $100. Kept it rather then give it away at those offered prices.
Everything you say here are my reasons except the Nexus 4. Androids lose value, The nexus don't really. They actually went up in value for a brief time when the phones got discounted to 199$.
In my market now, a used nexus 4 asking price is $200-$250 a used iPhone 5 are asking $200-$350. Depending when you bought the phone, you could have had a 6-8 times great lose reselling an iphone 5. Same with the Nexus 5, those things are going for 300$. There is no apple iPhone that every only took a $50-$100 hit.
The upfront cost is also a lot less for nexus or none at all in my case. If I wanted to an Iphone today I would have to get a plan 40$ a month more. Thats 1000$ more over 2 year plus an upfront cost of 265$ for the base iPhone 6.
For all other apple products and Iphones (compared to non nexus) apple has great resale value.