Aside from all the discussion about remaining in gear, finding the bottom of the shift pattern easier etc… from a practical standpoint, you don’t want to have to shift down into first gear when coming to a stop. It’s typically pretty low and that can make for a rather awkward stop at a reasonable pace.
To shift through gears in a manual gearbox, you disconnect the gear you are in, then connect the gear you want to be in. Being in two gears at the same time is impossible, it would lock up the gearbox and break something.
This means there is a neutral position between every gear shift. The neutral position between first and second is the most useful, so the shift drum has a detent for the ball (the thing which “clicks” and stops the shift drum, it’s usually a spring loaded ball which clicks into a detent). Since you want to shift fast from first to second, the neutral position is left in between the shift lever stroke, so finding it is sometimes a bit more problematic.
Some bikes do have a different setup, like neutral under first gear. (I think that’s what the super cub does, which is actually the most mass produced bike in the world…).
Clutch neutral is always on hand, so tucking that away is more practical and makes it less finicky on the gearing.
To me, having the first gear at the bottom makes takes all the guess work to drop gears all the way if coming to a stop from high gears when there’s less time to gradually slow using the lower gears.
Most of the responses that it’s because “safety” – harder to unintentionally neutral – sound like it makes sense.
But the actual answer is that the most common transmission and shift drum design has neutral between every gear – the shift dogs must free wheel between gears to be able to engage, and putting the extra clearance and neutral detent between 1 and 2 is simpler and more compact than extending the shift drum and transmission to accommodate a neutral elsewhere, e.g. N-1-2-…
In fact MotoGP bikes which use reverse “GP shift” going up 7-6-5-4-3-2-1 … N – but they must activate a lever (or switch these days) to be able to engage neutral. They do this so the shift gap between gears is absolutely minimized and completely consistent, for that little bit of competitive edge, and that makes it worth designing a more complex transmission/shift drum/neutral.
It is a nice feature, though, that you can’t just hammer the shift lever down into Neutral on most bikes, but that’s not the primary reason.
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