I've found the same to be true with my engineer. At first I thought it was just me who was using a weak build since I started out trying to maximise survivability by taking pistol and shield. However it took ages to kill single mobs and the gain in survivability was negligible since, more often than not, getting out of combat quickly is the better option.
Then I switched to a rifle build and straight away got confused. Using a rifle is meant to be a ranged weapon and so therefore should have you fighting at range. Yet an engineer only has 3 damaging attacks with a rifle and two of them require being very close to then enemy. So you have a ranged build that isn't ranged and does less DPS than a warrior using a rifle.
Ok I'll try a weapon kit instead. The only build I've found to be viable is a very cheesy flamethrower debuff setup. But even then I do less damage and have less survivability than a thief or ranger who plough through most mobs whilst I'm busy wondering why, as an engineer, all my engineering skills are worthless.
Damn, that blows. The Engineer was the next build that I was going to try. Well, thanks for the heads up. I guess I'll go with my Necromancer instead as my 3rd one. She's graduated from a glorified bank slot now.