A four cylinder will typically run smoother overall.
While you do have two going up and two going down @ the same time, They are on opposite ends of the 4-stroke cylce. One is on compression and the other on exhaust. One will be on power strole while the other on intake. Most 4-strokes the cylinders will be paired 1-4 and 2-3.
On gas engines, they use 2 coils. Each coil feeding a "pair" of cyls. The coil fires eache time the piston is @ top dead. Even if it is on exhaust stroke, cause its "partner cylinder" is on compression.
All engines are balanced according the the reciprocating and rotating weight they are slinging around. If you hooked an external power source to a 3cyl and a 4cyl, there would be no difference in vibration since they are both balanced.
The more vibration on fewer cylinders come from fewer power strokes per revolution. On a 3cylinder, it is 120* between fires. On a 4cyl it is 90*. Each time you have a power stroke, the gases srive the piston down, and then it requires the stored momentum of everything to continue spinning to the next power cycle. A 3cyl has to use more of this stored momentum. It is too much to detect by us, but the motor will actually slow down between fires, and then speed back up once fired.
Since most engines open the exhaust valve (signaling the end of power stroke) at about 5-10* BTDC the engine is really only making power for about 80* of the power stroke. On a 4cyl, that leaves 10* up to the momentum and 40* on a 3cyl. These very high frequency speed-ups and slow-downs happen at a higher magnitude in a 3cyl. That is why the seem to vibrate/run a little rougher.
A perect example of this is the Motorcycles of the 70-80's. Most were either single cylinders, or two cylinders in V or in paralle. While they ran good, the inline-4's that were comming into play were night and day smoother.
