Here are the possible options for change:
1 - Magic Missile no longer ignores SR and follows the standard d20 rules Hero
2 - Any meta magic feat that alters or add to the nature of the spell's damage type eliminates the no SR. So burning MM get SR but maximized, extended etc. still no SR. I would apply this across the board because SR is comparatively rare and pretty easily overcome. Whitesword, Valdis, Asinjin, Windblade
3 - A spell that has one of the 'fancy' feats attached ignores SR, but the feat attached must overcome SR to apply