how about some better maths, instead of assuming they hit the same number on the table, lets assume they have the same roll and the same ability
There is nothing wrong with the math I provided. I specifically stated that larger weapons were better against DR creatures and breaking supernatural shields. The former only gets a d100, and the latter takes damage for when the weapon fails to hit.
I make 2 attacks with a 2 handed axe, of 100 damage, with a -40 penalty to each one, and I make 3 attacks, with a Hand Axe of 45 Damage, with a -40 penalty to each one. I have a strength of 10 for this purpose.
Now let us assume that all d100 rolls are identical, and let us also assume that the first attack strikes at the 50% damage range. With the 2 handed axe, this will cause 65 damage on the first hit, then, on the second hit, because of a -30 penalty to defend, I'll cause 80% damage, or 104 damage, for a total of 169 damage.
With the normal Hand Axe, I will cause 30 damage on the first hit (50%), then I will cause 80% damage on the second hit, or 48 damage, then I will cause 100% damage on the third hit, or 60 damage, for a grand total of 138 damage.
169-138 is a measly 31 points of damage difference, between two weapons that have an enormous damage differential, on rolls that I wouldn't consider sucky at all (138 damage on a single attack action is really really good).
Now try a single attack a full attack value, which is the best coarse of action in many situations, such as overcoming someone's Defense/Projection, particularly on opponents who have powerful supernatural Shields or can defend multiple times without penalty. The two handed weapon wins cleanly in these situation because it has much higher base damage.
In the scenario you proposed above, you are taking the situation were the lighter weapon is supposed to have the advantage (multiple attacks to lower an enemies defense), so of course it comes of looking better.
The slower weapon still has the advantage, a little, but were I to say, dual wield ambidextrously a second hand axe, I would get to make yet another attack for 110% damage, after offhand penalty + 4th defense penalty, causing a grand total of 204 damage for the dual-wielding hand axe guy. If the dual-wielding hand axe guy isn't dual-wielding, he probably has a shield, giving him increased defense ability in return for causing 31 less points of damage than the 2 handed axe guy.
All in all, the new rule is very well balanced.
You can dual wield many larger weapons with sufficiently high strength, adding ambidexterity into this really does nothing. Someone with 11 Strength could simply dual wield two-handed swords and come out ahead.
While using a Shield can also apply the above just as easily since large weapons don't have to be wielded with two-hands with sufficiently high strength. Also, taking a shield may increase their defense, but it also takes an additional proficiency + gives an initiative penalty of its own.
Not to mention, many large weapons have less apparent advantages, such as higher fortitude/Breakage/Presence.
I'm not saying that the two-handed weapon is always superior, but it has its purpose. The new rules actually gave a big boost to smaller weapons, which in my experience are rather unfavorable under the original rules unless you were equipping a low strength character focused on speed/stealth over damage output.