First, what the heck is the "quality" factor for a part? It doesn't appear to do anything other than control the up or down arrows.
I have several "common" weapons which do more damage than purple and even epic weapons on a per second basis, but the up arrow shows up on the epic ones simply because they have a higher "quality" number. The common weapons are clearly superior due to the enhanced DPS. For example, I have two one-handed pistols at rarity "better" which do above 17 DPS and attack very fast. I have a two-handed cold-shot rifle which does 17.1 DPS at normal attack speed but is listed as rarity "artisan." It shows up as a better weapon option than equipping the two one handed pistols even though the two one handed pistols do twice the DPS. Yes, the cold shot rifle has some extra attack it can do, but it has a 45 second cooldown on that and at most it's 100 extra damage every 45 seconds. That assumes a rank 4 mech. That only adds an extra 2.2 DPS. Yes it also freezes for 4 seconds. But big whoop. I can kill every enemy servo twice as fast with the two pistols and that gets me far more time without them shooting at me than the 4 second stun does. And it always works like that, without me needing to remember to do anything. So, those two pistols at 17 DPS are always going to be better than the two hander at 17 DPS with the extra stun shot. And, even one pistol with a shield equipped is better as it reduces incoming damage significantly. No matter how you slice it, that artisan part is nowhere near as good. I also have a two-handed "common" rifle which does 42 DPS and the Artisan part is listed as better than that one. The same logic applies. 42 DPS vs 17 DPS ... there is no way the Artisan part (though higher "quality") is a better option to equip.
I have several volley pods of various quality and I have two Epic Stun Grenade Launchers. Again, the Epic falls far short of the common volley pods. The volley pods dish out 300 - 450 damage per round in a large area and have great range. Yes, they have a slow cooldown, but they can clean up enemies like it's nobody's business. The Stun Grenade has limited usefulness. IF you can manage to hit what you are aiming for before it moves out of the way, you can technically stun a ton of enemies and then hit them with a volley before they move. Except, the stun grenade is so slow at launching that they are almost always out of the area before it lands, so it's rather hit or miss on whether you stun anything, much less a large group of enemies. The stun doesn't last long enough to do serious damage unless you can follow it with an immediate volley of missles or two. But the stun grenade launcher is an epic part and the volley pods are common. So, the stun grenade launcher shows up as an upgrade to the volley pods, even though the volley pods are clearly superior.
Armor seems to not be too helpful. I built a melee servo which was decked out with the highest armor gear I could put on him (he had armor just over 20) and gave him an Epic drill and shield. I could tell the armor was reducing incoming damage, but not enough to outweigh the fact that he has to stand there being bashed on by tons of mobs. Giving him a ranged weapon and replacing the armor with volley pods made him much more survivable as I could just walk him around the map and dodge incoming attacks and snipe enemies. So, either armor usefulness needs to increase, or melee weapons need to do a lot more damage to compensate for the close quarters fighting with so many mobs.
Secondary effects are what exactly? I have a thing which protects me from them for 7 seconds, but it never seems to do anything useful for me. It's listed as better than almost every piece of gear I can put in that slot, but it seemed totally useless. I thought maybe corrosion or fire or something, but there's no way I can trigger it on time to protect against such attacks on a per-attack basis, at least not unless he's my only servo to control. It either needs to work all the time or it needs to go away. It's certainly not very useful at the moment.
