Since I am new to wordpress plugin development I have been examining internal structure of many plugin's and I could find most of them doesnt fit any pattern and understanding how they works is pretty much difficult. I was wondering if there is more generalised way of plugin development, possibly with a framework, other than the methods discribed in official documentation.
AFAIK, there's no
I'd say WordPress Coding Standards are a blueprint for a good style.
You'll find lots of good examples and excellent coders here in WPSE. A nice starting point: questions/tagged/plugin-development.
[ update, thanks to @Wyck contribution, a list of helper-plugins/boilerplates/frameworks ]
I believe Sunrise (http://gndev.info/sunrise/) is the kind of thing you're asking for. It's relatively new, and I haven't used it myself, so I offer no recommendations. However, it looks quite promising. It's available on WordPress plugin directory as a plugin: http://wordpress.org/plugins/sunrise/.