By my reading of the document, it would seem you are assuming that people roll for initiative every round?
This would be the only way your modifiers make sense. If you use one initiative per combat, your system is "Realistic" for only the first round.
How can I say this? Well using a weapon also depends on that weapons weight, the combatant's stamina and strength, and the duration of the combat.
A perfect example would be the movie Rob Roy. The final duel between Rob and the fop. Rob Roy uses a very heavy weapon and is extremely tired at the end, while the fop, although tired, is much better off than the scottsman. Rob is the hardier of the two men, having grown up on the land, but his weapon is extremely heavy.
In addition, CRGreathouse's comment on weapon lengths is extremely valid. But even then you'd have to take into consideration the speed at which the combatant with the greatsword could bring his weapon to bear. The greatsword's swing is difficult to control. In fact once a greatsword wielder swings the first time, a dagger user could duck in and stab repeatedly before the greatsword wielder could stop his swing and bring it back for another attack (even if he attempted a backswing attack). I am of course assuming both combatants are of equal training.
This brings up the factor whereby a wizard with martial proficiency greatsword is nowhere near as good as a fighter, no matter what you might want to say. The BAB reflects this well, however you should factor that into any form of initiative modification system.
Yes what I am saying is to not even try ... I agree with Hammerhead and CRGreathouse ... the core rules work well, all beit with a light suspension in reality, however there is basically no simple way for you to simulate realistic fighting. If you really want a system like that try Rolemaster which doesn't even do it 100% unless you use one of the myriad of optional initiative rules out there.