Back in the 8-bit days (C=64 vs Atari 8 bit like the 800XL) I was an avid Atari fan with Commodore being the 'arch-rival'. Back in those days the comparisons/competitions were close between the two machines.
When the 16-bit giants entered I balked at the Atari's offering...the Amiga wiped the floor with it. Undeniable to even a devout Atari fan (and C= basher, back then) like myself.
The OSes, as mentioned, were worlds apart in fluidity with TOS being a kludgey, non-multitasking nightmare compared to Workbench.
The Amiga's OCS/ECS chipsets delivered rich 4,096 color HAM graphics as opposed to the ST's feeble 16.
The only advantage the ST had in my opinion was the inexpensive 1040 and 520 ST models which were (at least before the release of the Amiga 500) far cheaper than the A1000.
Arguably, this made those little machines ideal for the music field, being inexpensive and coming with MIDI as standard ports.
The MegaST was Atari's attempt at big boxing these machines, and in my opinion, was not anywhere near as usefull as the A2000 was at it's time (which in a sense, was a big box version of the A500).
The higher clockrate (8MHz vs the A500/A2000's 7.14MHz) 68000 did little to improve software performance.
Finally, the A2000 is a far more expandable machine as well. If you really juiced it out, you could have an 060, SCSI, graphics card, ethernet, and even USB onboard. I'd like to see an Atari MegaST come anywhere close to those specs...even the Atari Falcon only made it to the 030 cpu, and I think only the ST clone Hades is the only 060 based Atari compatible out there. Correct me if I'm wrong, I don't know a heck of alot about the ST line of Atari computers.