The 6502-based Atari computers had the CPU clock held at 80% higher than the C64. That must have been a very significant impact at a time when the CPU had to do most of the work.
The PAL C64 was actually slightly under 1Mhz but you had a lot more VBlank time to do stuff.
The lower resolution also means less time plotting pixels so for any sort of software rendered effect the Atari machines are miles ahead.