That is an idea too. As
@Maxperson pointed out, historically magic resistance wasn't any less effective against magic missile, power word kill, or similar spells. So I was thinking of just making it the typical MR save (save throw + modifier + MR). Is that to much in your opinion?
While that is how it worked historically, the systems have changed. In 5E, those spells were not
meant to have much (if any) defense against them, so I probably wouldn't add a modifier to the save (after all there is no save currently, so you'd have to judge for each one what to use for the ability).
Consider the simplest option:
magic missile. Unless you have the
shield spell or a magic item, in general you are just going to take the damage and suck it up. At the highest levels, the normal maximum save DC is probably 19. In your example with a creature with MR +4, a 15 or better (30% chance) would be immune to a particular casting of
magic missile against such a powerful spell caster. Against a weaker one with a lower spell save DC, the odds improve nicely to 65% vs DC 12 (the lowest DC in all likelihood). Even with a lower MR of just +1, such a creature has roughly a 50/50 chance to be immune to such a spell
without adding ability modifiers to the saving throw.
Frankly, I have always found it easier to play test the baseline feature and if it is too weak, buff it, than it is to struggle with an overpowered feature and figure out just how much to pull back to balance it.