Question: why didn't any of these issues prevent the web from taking over the desktop during the years between 1995-2005? Native has always been faster and more feature rich, on every platform and at every point in time.
Individuals control most phones. The goal of the developers is to intrude on your device and you have permission to allow it.
The issues here are same as "web toolbars". Developers want to intrude on your mindspace and the web doesn't allow that easily. Consequently, they have no incentive to build good web apps.
1) Microsoft made Windows too damn fragile. Installing the app means that setup.exe will write all over the hard drive, and uninstall was never easy. Web didn't required install/uninstall.
2) Windows programs, with a few notable exceptions, were/are butt ugly. Web started as an ugly abomination, but designers catched up quickly. Web applications, even then, on slow connections, often provided more pleasant experience.
Web app on mobile today doesn't have the same luxury - native app install/uninstall is painless; native applications are better integrated and most of the time handle unstable connections better; good native apps are beautiful and often have superior usability compared to web apps.