However well designed it is, the gearbox on a big engine, particularly a single, will never be as smooth as a small engine.
When the bike's ticking over at a standstill with the clutch engaged, both sides of the clutch and approximately half the gearbox is connected to the engine, and thus spinning at some speed. The other half of the gearbox is connected to the rear wheel, and thus is not spinning.
When you pull the clutch in and knock it into gear, you've got to connect those two halves of the gearbox together, which means the first half has to stop spinning. Since it has mass it also has rotational inertia, which means it wants to keep spinning.
The more torque a bike makes, the bigger the clutch and gears will be to cope with that torque, so the more inertia they will have. The bike itself also has inertia, which is why if you push it around it's hard to get it moving, but once it's moving it's hard to stop it (without pulling the brakes).
Imagine you have three marbles, a big one, a medium-sized one, and a small one. The big one represents the bike. If you sit that one on a table, and roll the small one towards it, when they collide the big one will hardly move - the inertia of the bike is much greater than the inertia of the gearbox internals. Roll the medium-sized marble at the big one at the same speed, and the big one will move a bit more - the bike with a heavier clutch and gearbox is more able to jolt the bike forwards when you engage gear suddenly.
Apologies if I've over-simplified this to insulting levels. It's a bit tricky to guess someone's knowledge of physics over the internet!
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