It could be that the whole combo is better, but anyway, here is the idea behind skipping cleave.
The average damage/blow min-max calculated from the skill descriptions as they show in my skill panel (current cutlass level 2) gives
Whole combo: 29-58
Without cleave: 30-61 (slightly better, even)
So they are pretty much as effective. After 20 mouseclicks you've gone through the whole combo sequence 4 times and through the "without cleave"-sequence 5 times and then the total damage delivered would be
Whole combo: 580-1168
Without cleave: 605-1225
Don't know how upgrades affect this, but I doubt it makes a big difference either way, if skill points are allocated here. Maxing cleave probably does some good. However, leaving cleave unlocked saves some skill points for other uses.
Simon