Pick a weapon expertise based on your own preferences. I went with duel wielding simply because that wasn't an option in Divine Divinity or Beyond Divinity.
If there is a significant difference in damage per second between the two (mentioned in the
Character Optimization topic IIRC), it would not be enough make a huge difference to your character. If they can survive using level 1 expertise rather than 4 or 5, then I'm sure they can manage with either weapon type. After getting the battle tower you can also unlearn your skills and reinvest the skill points, though the price doubles each time you do so (assuming you collect loot to sell, you should be able to get enough gold reskill up to 3 or 4 times without too much effort).
With the latest update of the game, opponents in the swing arc of a weapon will be hit, as well as the target. Some of the negative comments about two handed expertise may have been based on earlier releases of the game.
It doesn't matter which weapon type you pick, you will find good weapons of the opposite type. I played a duel wielding strength based warrior, and generally didn't pay too much attention to two handed weapons, but did notice a couple very nice ones. More of an issue was finding an abundant supply of magical and balanced damage types on weapons, when trying to get ones doing conventional melee/ranged damage (don't recall a big issue with random loot, but IIRC at least the couple merchants in Aleroth seemed biased towards magic).
