Now, I agree with the last sentence.
Making women equal to men (in strength and size) is fantasy, but fantasy which not many will raise a fuss over.
So it's probably the best course for Obsidian to take and probably the course they will take.
But to the first one... sheesh.
Suggesting that men tend to be bigger and stronger than women, is not a stereotype. It's a fact.
I will not dispute that this is a statement of fact. I will say that it is a useless fact. There seems to be a lot of fighting over the right to make that generalisation. However, once you begin to examine any specific scenario and the specifics thereof, there is no value to a generalisation as it could just as easily be the case as not be the case. To use the case in point - it does not matter whether or not on aggregate men are stronger than women if you are dealing with a particularly strong woman.
Also, the factors that contribute to strength are many and varied, and statistics that are being used are all being gathered from a scenario where strength is not often valued in women and as such rarely pursued, and when pursued - by only a very small percentage of the total female population. When you are considering factors as changeable as the density of muscles fibres broad generalisation offer nothing but a sound-byte.
As for character creation, I imagine you will begin the game 'in medias res' rather than at birth and as such any character (female or otherwise) will have made the decision to pursue a set of skills and abilities, and will have trained and practised appropriately - surely this alone is enough to remove the need to conform to the generalisation?
As far as plot points go, I don't see the need to cling on to sexual discrimination and such when there could be so many original reasons to hate people in a fantasy universe. If I roll a female wizard I'd be disappointed if the female part was singled out.