That is what I look at - numbers. So it depends on the ship also: My Viper MKIII can stay behind most NPC's where the FGS can't and is longer range type fighter. So then it comes to your fighting style of strafing runs with MC's or a few long range shots from distance, but the engineering of MC's is better hmmm.
I just started my engineering so it really wouldn't hurt to try them out and see if I can adapt to a different flight style.
The experimental effects of each type are useful in special situations. Giving precedence to use one weapon type over another depending on what the goal of your combat situation is. The unique experimental effects for each weapon are listed below. They do share some such as Auto Loader and Smart Rounds.
Cannons
Dispersal Field : experimental upgrade that causes successful strikes to temporarily confuse all gimbal and turret hardpoints on the target, at the cost of direct damage potential
Force Shell : modification to allow firing of low explosive shells, designed to generate a propelling blast. Strikes to a target are capable of forcing ships off course, at the cost of shot accuracy.
High Yield Shell : modified munitions that convert a portion of damage to explosive, capable of hitting multiple internal modules if the attack breaches the hull, at the cost of a reduced fire rate.
Thermal Cascade : experimental munitions that interact with shields upon detonation, generating significant heat on the target.
Multi Cannons
Corrosive Shell : experimental rounds that temporarily weaken
Armour Hardness and increase all damage taken, at the cost of reduced ammo capacity.
Emissive Munitions : experimental upgrade that causes strikes to envelope the target in energetic particles, significantly amplifying its signature, at the cost of increasing heat generation for the attacker.
Incendiary Rounds : modified ammo system capable of delivering superheated rounds, increasing damage and converting a large portion to thermal, making it more effective against shields.
Thermal Shock : articulated focus array designed to spread heat effectively. Strikes to shields and hull impart additional heat into the target, at the expense of a 10% reduction in damage.
Using a Turret Cannon with Dispersal Field on a large ship acts very much like a backup chaff launcher. Or adding Incendiary Rounds to a multi cannon to compensate for not equipping any lasers to strip shields.
But it quickly becomes pretty obvious why most use the Corrosive Shell of the Multi cannon, because it stacks with other damage, where as most other effects do not directly aid in increasing damage.