The problem is: A lot of the 'native' libraries and even the open-source embedded RT OSs really suck.

And if you use a vendor's library you are very locked in: Let's say you use a TI chip for your prototype but then someone who knows stuff about designing hardware tells you that now it has to run on an Atmel processor because $profits... you will have to reimplement a lot of your stuff which costs (quite a huge amount) of time and might even require an entire rewrite..