Why the app store hate? My work computer needed an OS re-install recently (learned to be careful with sudo) and then they bought me a new computer shortly after

Why the app store hate? My work computer needed an OS re-install recently (learned to be careful with sudo) and then they bought me a new computer shortly after. The app store made it easy to re-install a bunch of my apps like Evernote, Aperture, iWork, etc., and the app store keeps these constantly upgraded. Then I had to go through and download a bunch of other non-app-store apps (MS Office, ImageJ, Matlab, Adobe suite, Canopy, etc.), and these apps are always popping up with their own custom update software to remind me to update them when I open them. I think it would be great if I could just use the app store to keep track of all my software, easily install and uninstall it on different machines, and keep it updated in the background.