Nexus devices have a variety of manufacturers. The current 9 is made by HTC, the 5X by LG, and the 6P by Huawei
>one company provides the software
Nexus devices all come with unlockable bootloaders that allow you to flash custom Android ROMs such as Cyanogenmod. Past that, other operating systems such as Firefox OS and Ubuntu Touch could be flashed on Nexus phones such as the Nexus 5.
>app store
F-Droid is an alternative FOSS app store available for Android. You can also use Amazon's App store which is what Amazon's Kindle Fire Android tablets do rather than Google's.
You have realized that from Android M on you can’t rely on getting notifications on Android anymore unless they go through Google?
Any application running in background – unless it is from Google – can be killed at any moment to save battery.
In Android M, when the device hasn’t been used or moved for half an hour this "Doze" mode activates, usually during the night.
In Android N, it activates as soon as the screen is off.
I find it extremely annoying that android devs assume this, because apps fail to install/work when one doesn't have google play services installed.
Obviously only the latest matters?
And those are manufacturers, not the company designing it, which what matters. Otherwise Apple uses a variety of manufacturers too, not just Foxconn.
Long story short: just because you can doesn't mean you must. Options are nice but so is not having to think about it. The Nexus is a middle ground for Android
Apple relatively recently removed the requirement to pay for a developer account to compile and run apps on your own device. You can pretty much sideload apps like you can on Android, just with the added requirement of re-signing them for your device specifically (which is IMHO a nice security feature). A lot of the app store rules are enforced by human review (e.g. only being allowed to use background execution for certain things), not the sandbox itself, so you have a comparable amount of flexibility (one thing I still really miss is the ability to do JIT and dynamic code generation).
I value reliability over everything else and in Androidland, that means Nexus devices with zero customization.