TOS was based on CP/M which MS-DOS was based upon.
If Commodore wasn't in such bad financial shape, the machine they were going to release (aka the A3000+) would have kicked the Falcon's arse! But due to Commodore's lack of funds (and idiots running the company) they made made the cut-down AGA chipset/A4000 design. A big mistake was the fact they didn't make a 16-bit Paula. They should have at least kept the DSP chip design they were going to use on the A3000+ and put it into the A4000...
I do think the A4000 is a superiour machine in terms of the OS and the fact it had expansion slots, where as the Falcon was a step back for Atari by not giving it expansion slots in the first place. I believe Atari did make a prototype Falcon which did have expansion slots, but it didn't see the light of day of course. The Falcon does seem to have better hardware (DSP, and the 65,000 colour mode etc), but the A4000 can (and has) gone beyond what any Falcon can do, due the fact it has the capability to be upgraded in the first place, so I think the A4000 wins overall IMO.