Two fantastic machines !!!
I still have both.
Atari is more simply made, poor architecture, no custom chips so overall graphics and sounds capabilities are not as good as the Amiga(s). Simpler to code too (on first approach ...). And true first demos, first stunning gfx effects were coded on Atari first coz the challlenge was big : how to push the limit of this little machine ...
On the other hand, during the early good old days, games development on Amiga were often badly done : simply a kind of cross compiling with no true use of the custom chips, so games were slightly identical. But this didn't last too long, and "specific" games appeared : I remember a great change from the first release of Shadow of the Beast. I was 13 and and it was like a nuke fell down on our heads.
Well, this is my point of view ...
Giana