Robin2:
Thinking some more about the lack of Yun support I have been wondering is it wrong to think of it as a general purpose Linux computer. Perhaps it would be more correct to see it as having a very limited subset of Linux capabilities which were/are not intended to be enhanced.
Yes, for people that are getting frustrated with the Yun or wondering if it's right for them it's good to step back and look at what it's made to do. The Atheros processor does not run a typical full Linux distribution like Ubuntu/Debian/etc, it runs OpenWRT. Keep in mind there are only 16 megabytes of space available for the entire OS. The OpenWRT distribution is optimized for low overhead and size, so many common tools and libraries aren't available.
If you're looking for a full Linux experience, check out the Tre, Beaglebone Black, Galileo, Raspberry Pi, etc. There's more processor power and memory with those systems so they can run a full Linux distribution.
Don't think of the Yun as a Linux machine that runs Arduino code + shields. Think of it like an Arduino Leonardo that's supercharged with wifi and internet capabilities. You can use the Atheros processor to run python or other scripts that are good at parsing, network access, etc. which would otherwise be painful or impossible on the ATmega processor. If you think of the Yun as primarily a Linux machine I think you will be somewhat disappointed.
As far as difficulty using the Yun, unfortunately there's no magic fix in my opinion. Getting two processors to work together is not easy, especially when they don't share any memory and can only pass messages through a serial bus. The Bridge library does a pretty good job of hiding all this pain, but at the end of the day there's still a learning curve to working with multiple processors.
IMHO you'll be happiest when you learn to live with the limitations and realize the strengths of the Yun. If you're trying to do something that talks to a lot of USB devices and hosts a web page on the internet, the Yun probably isn't the best choice and a Raspberry Pi or other would work better. However if you want to read a sensor or talk to a chip that has strict timing requirements (like lighting NeoPixel/WS2811 LEDs) and make that data available to a web page, the Yun is perfect because it has the ATmega processor for realtime stuff and the Atheros processor for simple web or network serving.