Well, basically work equals force times distance. You've decreased your distance by not going all the way down. Think about it, if you bench press the bar from the barbell supports to full extension and that's all, you could bench probably double what you can now.I've heard taking arms below parallel is what puts your shoulder joint in an awkward position and increases your likelihood of a rotator cuff injury
I switched to parallel and my bench has gone up 20 lbs