Ok, here is a summary of the difference between the one-handed military weapons and their two-handed analogues.
The Handaxe, shortsword, war pick, and throwing hammer have no two-handed analogues.
battleaxe --> greataxe: +1 damage and 'high crit' property
flail --> heavy flail: +1.5 damage
longsword --> greatsword: +1 damage
scimitar --> falchion: +1 to hit, +0.5 damage
warhammer --> maul: +1.5 damage
It appears that the general trend is that +1.5 damage is a decent bonus for a weapon increasing in size. The high crit property is equal to about 0.5 bonus damage (my own numbers have shown that the high crit property is in fact worth about this much). Also, since high crit and bonus weapon damage both scale with tier (higher [W] powers, increased bonus from high crit, and increased chance to score a critical), the damage increases do not become trivial at higher levels.
There are two exceptions. The scimitar sees an increase of +1 to hit and +0.5 to damage when it becomes the falchion. The other is the greatsword, which gets a mere +1 increase to damage. In my opinion the scimitar sucks. It is a longsword that gives up +1 to hit for the 'high crit' property. It should be +3 to hit, 1d6 damage, high crit if anything. It gets a bit of an extra boost to make it balanced as a two-hander.
So why then does the greatsword see less of an increase over the longsword than the other greatweapons do, and why take a greatsword when a single feat lets you take the bastard sword, giving your the same [W] damage in one hand without sacrificing the +3 prof bonus (effectively, one feat gives you +2 to AC/REF).
I think the answer to this goes a bit deeper, all the way into the one-handed weapons. The balance seems messed up. Why would I take anything other than the longsword? I can either ditchteh +1 proficiency bonus for an extra damage (the axe/flail/hammer route) or I can ditch it for the high crit property (the pick/scimitar route). In my opinion +1 to hit is equal to about 1.5 damage. In this case the longsword is the superior one hander, and the balance issue with the greatsword comes from this:
1. The longsword is greater than the other one-hand military weapons by about 0.5 damage.
2. A two-handed weapon is 1.5 damage ahead of a one hander as shown above.
3. A superior weapon is about 1.0 damage ahead of a one hander:
longsword --> bastard sword: +1 damage
shortsword --> rapier: +1 damage (still light blade)
Then a greatsword should be 0.5 damage ahead of a bastard sword, but since it got less of a boost than the other two handers it is not. One option is to make the greatsword (1d6+1d4) for an average of 6 damage making it 1.5 damage over the longsword and 0.5 damage over the bastardsword. My opinion is that the longsword is too good itself. It is better than the other one handers, and since the bastard sword is based on the longsword, it is also too powerful (as good as a two hander, but in one hand).
Since we obviously don't want to change the longsword, I suggest we change other weapons based around it. This would require a complete reworking of the system unfortunately, which is a pain. I don't see any other way to balance it. As far as I can see the greatsword is not an option for fighters, and the longsword/bastard sword are the best weapons available.