I have a Yun, and have experienced some problems with it, especially the lack of information. Had planned using the Yun for a product prototype, but I believe that instead using a Raspberry Pi, which is both cheaper and packs quite a bit of power, in addition to having a very large user community would be the smartest choice.
Raspberry + Arduino = <3
Have a look at INO (http://inotool.org/quickstart), which for instance allows sketches to be uploaded directly from a Raspberry to any arduino.
/Christian