Application folders are as poorly thought out as Program Files was. Here's why:
Path inconsistency - Crack open a terminal and try to run your app from there. I'm sure environment variables have a length restriction, even if it's really long ;-)
Lack of security - try to patch all those apps using the same non-core shared libraries, you'll have one hell of a time as you'll need to either manually copy files or wait on the vendor!
Disk space wastage - see above! :D
Power-user hell - let's say you can do a little bit of coding, enough to work around a few small bugs; tried compiling larger XCode projects without manually replicating the dev environment?
Now for other flaws in modern OS X:
App Store - This is a poor man's APT/YUM repository. You can't mirror it so if your Internet is unavailable you can't install apps, plus you need to hand over personal info to use it!
Global menus - Modern systems have many applications running at one time, you need to activate the window before you can access the menu, thus increasing click count if multitasking.
Style inconsistency - OS X apps are inflexibly styled; so when the designers of OS X change fashion, the apps don't match. Compare this to most GTK/Qt apps, centrally rethemed easily!
Single mouse pointer - Linux and Windows can use multiple mice/tablets/touchpads independently with each having their own mouse pointers. Mac OS X assumes one pointer even today!