Additionally, I'd consider a typical two-handed weapon wielder, who by the use of 3.5 Power Attack can gain a solid +3 to damage per plus if they pool the bonus to hit pilfered from the bonus into power attack, compared to 3.5 on average per d6 of an energy enhancement. I also believe that you might be discounting the flexibility that plussed weapons offer, the choice between accuracy and damage. When making full-attacks that additional accuracy really does help. The two-handed weapon wielder also does not have to worry about dealing with energy resistances, which become abundant as levels escalate. With all that said, energy enhancements really are better for sword and board combatants, and two weapon fighters, most of the time. One solution to keep this phenomenon in check might be to rule that weapons may only have up to their weapons true enhancement bonus in bonus weapon abilities.