ummm, when it comes to operating systems, I never found /usr/bin particularly difficult, and dumbing things down to /Programs, /Users, /Files etc doesn't seem to really be anything other than a trivial and superficial aspect of an operating system. How they multitask, manage memory, keep the file system running etc - these are the tasks of the operating system. How apps get installed is largely up to the app developer. I can statically link and provide one simple big binary, or choose to componentize so that upgrades are less network intensive, but this is just the minutia. OSX already bundles everything into one place (for the most part) and most Unix systems are really easy to understand the structure, /etc for the configuration files, /var/log for the log files and /usr/[local]/bin for the app. libs to /usr/[local]/lib etc etc. Nothing particularly difficult about that. And there are some very good reasons for breaking things up and scattering them around. /var/log would, for example, often be a managed part of the file system, for log rotations and often on a different physical media to prevent disk head movement associated with the logging requirements from interfering with the main purpose of the app. /tmp would often be mounted as a very fast ram drive or some other high speed r/w filesystem type that an app can use for its temporary storage. /usr/bin would be backed up, /var/log, /tmp possibly not so...
There are very good reasons for how many operating systems have ended up the way they are, and simplicity isn't always a lofty goal. Take for example, the implementations of malloc/free. Its very important for these to be very efficient, very fast, very reliable and not at all simple. Simple is good in UI's (sometimes), good in many things, but please, keep simple out of the operating system design...
To a large extent, OS X gives the best of both worlds.
From the command line, things look very much like you describe (but not exactly, Apple often has different conventions and names for things than Linux, say). That application you just downloaded is just a directory with a ".app" extension. You can browse its directory structure and find all of the resources for the application, all residing in their conventional locations.
But using the Finder, you just see the application's icon. If you double click it, it launches.
This is just one of the ways that Apple manages to have Unix underneath, but not expose it to users who don't want to care that it's there.
There are very good reasons for how many operating systems have ended up the way they are, and simplicity isn't always a lofty goal. Take for example, the implementations of malloc/free. Its very important for these to be very efficient, very fast, very reliable and not at all simple. Simple is good in UI's (sometimes), good in many things, but please, keep simple out of the operating system design...