Windows 95 never had a proper, operating-system supported package manager, and I think that's a big part of why web applications took off in the late 90s/early 2000s. There simply wasn't any guarantee that once you installed a native app, you could ever fully remove it. Not to mention all the baggage with DLL hell, and the propensity of software to write random junk all over the filesytem.
Mobile has forced a big reset of this, largely driven by the need to run on a battery. You can't get away with as much inefficiency when the device isn't plugged into the wall.