On "why?" then it gives you an immediate and considerable library of software to play with, development options and most besides. No other reason or justification is needed.
The library may not be as refined (it is largely going to be java based), open, or specialised as something like Debian's ARM build or whatever emulator/game distro the kids are excited about this week but if the end result is programs which run in real time/useful timeframes for humans then that is what is needed here.
If the mere act of doing it offends your sensibilities then might want to look into that. Or were you all so blinded by the lack of anything on the 3ds compared to that which came before that you are blind to the potential?
Where are people thinking that? While I doubt many would be going home in the "gun to head, alter the kernel in this way" test (compiling might even be a push) and there have been some suspect comments, some getting hung up on odd things (thinking it has to replace the full OS when dual boot and hypervisors are options) but having just gone through it I am not seeing the "ease" set represented.
Custom junk? It is almost like we have never seen hardware reverse engineered and drivers made
http://archive.oreilly.com/pub/post/bountydriven_project_to_revers.html
https://www.raspberrypi.org/blog/quake-iii-bounty-we-have-a-winner/
https://learn.adafruit.com/hacking-the-kinect/overview