Would it be possible to modify the arduino sw such one can start/stop an application(sketch), and when stopped one can upload new one, but also via wireless uart (ie. bluetooth, wifi, etc.)?? So no rts/dtr for reset, only rx, tx. And a "zepto_os" instead of the bootloader with following functionality: ^C you stop a running sketch, ^R you start a sketch, ^U you upload a new sketch. or something like that.. p.
No, not really.
AVR microcontrollers NEED to be reset to download new firmware. That's a requirement whether you are utilizing a bootloader or an ICSP.
While technically the Arduino software, as well as the Arduino hardware, could probably be modified to provide some level of support for a ZeptoOS setup, the modifications would be so extensive that you would be better off just designing a system from the ground up as opposed to trying to utilize the existing Arduino products.
XMOS provides a dev kit that appears to be more suited to a scalable distributed processing framework. http://www.xmos.com/xk-1a
They also have quad core micros, but their quad core dev kit doesn't appear to be similarly designed for easy chaining together (though that's not to say that they couldn't be chained together)
What if you just use an atiny chip with a wireless receiver to reset the arduino?