That has long been one of my complaints about Rails. It creates a nice directory structure for the framework's objects. But there's no obvious place by default to put business/application "your logic". So then all that stuff gets wedged into huge controller and model files. (in the old days there was a division between 'business objects' vs 'data objects' etc)

#1 is definitely true. I had my own halfassed 'framework', and have dug into enough older web apps to know that everyone else had one too. (Or at least the smart ones did.)