Windows (and most apps) in OS X are generally intended to do one thing. Even monolithic applications used full screen like Final Cut Pro are often made up of windowed components. Even so, there are also single-window apps that are intended to be used maximised and work perfectly well that way, such as Logic Studio. The problem would only be if you tried to use an app differently than it's intended to be used.

For many applications it doesn't make any sense to maximise them on a large screen. Very, very few web sites are wider than 1000px, so maximizing a browser on a large screen is pretty silly. Even if the site has a fluid layout, wide columns of text are horrible for reading.

Other applications don't even make any sense maximized, like a chat client like adium or a password manager. Apps like a terminal that could be used either maximized of windowed work perfectly fine either way.

And with software development the options are usually using emacs or vim full screen, which works perfectly well; using an IDE full screen, which works perfectly weel; or using a combination of smaller apps (eg, terminal, editor, SCM GUI, broswer, etc), which, despite being a different paradigm, also works perfectly well.

So, really, what are these scenarios when maximizing every window a) makes sense and b) is problematic on OS X?