In line with the idea that Spell Resistance should provide a bonus to saving throws, there should also be more levels of "success" when it comes to saves. The current system of full effect or partial/half effect is what makes the current incarnation of Spell Resistance appear useful - when you want to give a creature the chance to avoid being affected by a spell, and evasion and/or mettle seems thematically inappropriate, Spell Resistance looks like a good option. Varying degrees of success will complicate saving throws slightly (you'd need to check against two numbers for full/half/none), but it also removes the Spell Resistance mechanic. Those who like more granularity (like me) can even work off the base system to introduce additional levels of success, such as full/three-quarters/half/one-quarter/none.