Er...wait wait. 
Improved Natural Attack increases the damage of one natural attack as if one size higher. A grapple is neither a "natural attack" (which is very specifically defined in 3.5e) nor does it do damage in and of itself (though you can do damage IN a grapple, once it's been established), and is therefore ineligble for that feat.
I'm not sure I'm getting the problem here. A size level of difference results in a +4 grapple bonus to the larger. Just take Improved Grapple. The bonus from that is identical. A medium creature with Improved Grapple is at effectively no disadvantage against a large creature that lacks it.
Isn't that what you're looking for?

Improved Natural Attack increases the damage of one natural attack as if one size higher. A grapple is neither a "natural attack" (which is very specifically defined in 3.5e) nor does it do damage in and of itself (though you can do damage IN a grapple, once it's been established), and is therefore ineligble for that feat.
I'm not sure I'm getting the problem here. A size level of difference results in a +4 grapple bonus to the larger. Just take Improved Grapple. The bonus from that is identical. A medium creature with Improved Grapple is at effectively no disadvantage against a large creature that lacks it.
Isn't that what you're looking for?