It's probably more the brakes than the engine. Diesel engines don't provide much of an engine braking effect (unless fitted with additional mechanisms a/k/a "Jake Brake" to provide this) so the vehicles use friction brakes any time they need to slow down, which can be jerky especially with air brakes. Electric buses would have regenerative braking which is probably smoother.
The vibration of the running engine is a big part of it. Very noticeable on diesel-electric battery hybrids; the whole feel of the thing changes when it's running on battery power.
