Just a random thought I had. What if, instead of each class getting proficiency in all saves with two of the six abilities, we brought back the old saving throw categorires: death/poison, rods/wands/staves, breath weapons, pettification/polymorph, and spells, and each class was proficient in all saves against effects in two of those categories? You’d still have saves with each of the six ability scores, but if you were proficient in saves against spells for example, you’d get to add your proficiency bonus to all saves against spells, regardless of what ability score the save was made with.
If one were to implement this as a house rule, I wonder if those traditional six categories would be the best ones to go with, or if it would be better to rejigger them slightly. For example, death/poison could become poison and disease, since there aren’t really a lot of save or die effects left these days. Rods/wands/staves could just be all magic items. Breath weapons and paralysis/polymorph are pretty narrow categories, whereas spells is extremely broad. Maybe those could get redistributed a bit to like areas of effect, transmutation (as in being transformed, not the school of magic), and mind-affecting?