I many ways, 3e's ideas were pretty sound from a simulation point of view. The level of the spell counted since higher level spells should be harder to resist than lower level spells. The offensive stat of the caster mattered because it makes sense that some casters would be more talented than others. Level affected the save bonus because more powerful characters should be more resilient than less experienced ones. Defensive stats mattered because some characters should be more talented at resisting than others. And, finally, it made some sense that character archetypes should be better at some saves than others and have stronger/weakers saves. They then set defensive resistance bonuses to be cheaper than offensive bonuses in magic item prices. That's all good stuff. But put it all together and add in myriad ways to enhance casting stats and imbalances between single-attribute dependent classes and multiple-attribute classes that could be exploited in character generation and you've got some trouble brewing.
I don't like this "should" mentality very much. As you say, these are very good
from a simulation point of view, but on the other hand you can't first of all say that the whole game SHOULD be that much simulationist.
IF and only IF you want a good simulationist level, then your ideas above are good (although I'd still say COULD, not SHOULD, because as much as they are reasonable, they are all assumptions that don't ultimately need to be, magic doesn't have to work that way in all games).
How about everybody else tho, those who aren't interested much in this level of simulation? To support the idea of scaling magic, you have just added that (1) spell level must affect spells, (2) caster stat score must affect spells, (3) caster level must affect spells, (4) target stat score must affect spells, (5) target level must affect spells. That IMHO is quite a lot... The game could still function with NONE of these things. It would be a different game sure, but that doesn't mean the game wouldn't work, in fact it would work just fine.
I'm not sure they can make these into a module, because going this route they will certainly add different ST progression to different classes because it's more "simulationist", and once it depends on class, it's hard to play without it.