As a platform, neither have died as each has its dedicated fan base.
Other than clone 680x0 based machines produced in reasonably small numbers where is the atari going?
Therefore, I would say that as a platform amiga is healthier. We have not one, but two hardware successors, each using more recent technologies and off the shelf components. I dont see any son-of-atari Peg/A1 style systems. We had PPC cards that reached the production stage (IIRC there were atari PPC cards that never got beyond the prototype stage).
Even as a 680x0 only machine we have better emulations with systems like WinUAE and Amithlon that surpass any atari emulation I have seen. I wouldn't be surprised if we had a higher proportion of 040/060 users in our userbase too, but that is pure conjecture on my part.
Then there is AROS, attempting to run everywhere...
As a company, possibly atari is in better shape than amiga inc, but it is definately a mere shadow of its former self.
