That is really the only solution that guarantees equality.
That is, if two-weapon style mean that you would make both your main and off hand attacks as one "attack", you would deal your 1d6+Dex plus your off-hand 1d6 at identical times the greatweapon fighter deals his 2d6+Str.
In other words 2d6+Dex vs 2d6+Str. Identical. Both equally open to bonus attack optimizing.
Of course, since you actually make two attack rolls, this would make TWF strictly superior, and it would make the feat and the fighting style inappropriate. But it would make a start.
Not saying this is such a good idea it's worth pursuing. Just saying it's the only real fix to the imbalance.