I know this could be interpreted as a rules question, but I really am thinking of a House Rule possibility. I wonder if it wouldn't be better to change the SR system to be a bonus to saves made against appropriate spells. This would make it on roll instead of rolling against SR then Rolling a save. It just seems that is where SR is more appropriate.
There are certain benefits to transforming SR into a bonus on saves. You eliminate the need for that die roll, which speeds up game play. On the other hand, you'll eliminate 2 feats and one elven racial ability and have to replace them. If you try to replace spell penetration with a bonus to save DCs you run into conflict with the Great Fortitude/Iron Will/Lightning Reflexes feats. You will definitely make it easier for creatures that have SR to resist spells, as those creatures at higher levels have significant SR which I assume will become a respectable save bonus. In turn, casters that normally beat SR and then hurt the enemy with their spells will have a harder time using spells directly against foes. You will also need to reconstruct the spell resistance spell as well as the holy aura chain of spells plus maybe a few other things. Oh, and remind the players who have PCs with SR about their save bonuses, giving them one more number to remember.
I think that sums things up;)
To complicated is what it boils down to. I have too much on my plate in converting stuff to worry about this, lol. Luckily it mainly comes up in my games when I take the players against monsters with SR. Oh well, I think I will try other things. Maybe somebody can create rules for SR that are akin to the Combat Maneuvers. Everybody gets some kind of magic defense & casters have a magic attack.