Currently, if you offhand wield something, the hit dam from
the weapon is counted towards your first wield. I also believe
that you hit just as well with your off-hand (limited only by
the success-rate of dual wield). I propose that fighters have
a penalty to hit with their offhand, as well as a seperate dam calculation
for the offhand.

Definitions:
Base (+hit +dam from stats)
Primary (+hit +dam from primary weapon)
Secondary (+hit +dam from secondary)
Penalty: A penalty to hit because you are using
an off-hand.

For your primary weapon:
base + primary

For your secondary weapon:
base + secondary - penalty

With this, I also propose that wielding a two-handed weapon
with both hands would be advantageous to landing hits and adding damage.
Polearms and Spears and Staffs are already like this, but I am
not sure if two-handed weapons (like swords) are.

If nothing else, I believe two-handed weapons should add their
hit-dam bonus' twice.. to be on par with dual wielding.

In my opinion, dual wielding really hasn't enough of a disadvantage.
There are too many situations where the great big boost to damage
far outweigh the usefulness of a shield.