Just speaking for myself here, but my clocking preferences preferences would be:
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Gates - but gates that are closed when Run is not enabled. Why a gate? Gates can save you some modules when you’re sequencing, but if I’m not running, 999 times out of a 1,000, I’m not going to want the gate to be wide open while stopped.
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Resets that occur on run. I know some sequencers will count the next clock after a reset as 1 and some count the reset as 1, but the former is just not intuitive IMO. That’d be like if DAW playback went to measure 1 beat 1 on stop, and jumped to measure 1 beat 2 on play. It’d be much more intuitive for everyone if turning off a Run worked like a stop, and hitting Run worked like a Reset+Play where beat 1 equals the Reset beat, then followed by beat 2, etc.
If Clocked included a “Gates closed on Stop” mode and a “Reset on Run” option, in addition to the current settings, it would be the be-all-end-all clock for me. You could then cover all the common use-cases, and if you were running two sequencers that counted beats after a reset differently, you could just run two instances of Clocked with different settings, but otherwise in sync to cover both types of sequencer.