Robin2:
I haven't used a BeagleBoard or a Pi but the BeagleBoard website doesn't seem to contain warnings against upgrading the operating system.
Personally, I don't expect the warranty on these things to last much beyond powering on.
I bought a BeagleBone Black middle of last year and still haven't done anything too useful with it. It is undoubtedly a powerful board but not exactly easy to go 'off menu' with. The website documentation is not complete by any means. There is a community but you need to be speaking their language before most anyone will deem to talk to you.
I got a Raspi last month. A great way to get going with Linux and programming. A great community, focussed on beginners. I haven't done anything on the GPIO side yet though. WiFi can be painful and I haven't had much success running it headless. The Pi uses a lot more power than a Yun and often ends up needing KVM interaction. I am not entirely convinced about relying on an SD card to boot a headless device.
My wife bought me a Yun for Christmas. I had my first web enabled project running over WiFi within a couple hours and still found time to cook the turkey. On New Years Eve, I published a link on my Facebook page and had greetings from our friends across the World, popping up on an LCD.
For the last six weeks, my Yun has been running a temperature and humidity monitoring web site, logging to SQLite, using NGinx to serve PHP, charting with Java Script, all over WiFi. It has gone up to three weeks between restarts. I made some changes to the PHP over the weekend and it's a bit unstable at the moment but that is is down to my programming, rather than the device.
I can not comment as to why people are having the game breaking issues they say they are having. The Yun has a learning curve but I haven't found it any worse than the Linux learning curve in general, the Pi in particular and no where near as steep as the BBB. I am now on my second Yun and a new Internet of Things project.
The biggest issue I have with the Yun comes from the choice to pair the SoC with a Leonardo. The SoC has a mass of potential, bottlenecked by the Leonardo's cheap MCU. The com port disconnects when a sketch is uploaded and doesn't always come back. Thankfully uploading a sketch over the network will usually sort it but significantly slows down my productivity. The lack of program memory is an even bigger issue for me. With Linux in such easy reach across the bridge, sketches are begging for string handling and OOP techniques. By the time the Yun library classes are loaded, I am having to worry about the number of function pointers needed for my own classes. I have had to refactor code, removing references to the F() macro, to trade SRAM for progmem.
What I would really like to see is a Yun version of the Mega, or even better, the Yun SoC as a separate board. I would also like to see an easier way to get started cross-compiling for the Atheros chip.
Anyhow, just thought you might like to hear from someone who has all three of the devices you mention and thinks the Yun is pretty brilliant.