The problem with Magic Resist is that the items don't defend vs. different types of magic damage
With armor you have passives that scale multiplicatively with other defensive stats. Thornmail is super effective vs. champions who deal raw autoattack damage with a lack of on hit effects, while Omen and Frozen Heart are great vs. champions with mixed damage on hit effects. Most magic resist items only are effective vs. burst damage.
Banshee's Veil is much more effective vs. someone like Annie than Cassiopeia/Vladimir/Azir Hexdrinker's shield is also much more effective at defending against burst.
In Season 2 this wasn't an issue because we had Force of Nature. Force of Nature did not give any health or spellblock, and a huge part of its power budget was in its high regeneration. This meant that champions who relied on burst were not hurt by FoN nearly as hard as champions who relied on dealing DPS.
There's a reason Cassiopeia/Ryze/Azir/Vladimir/Rumble have been top picks lately and almost every single one of them was nerfed in the last few months (some multiple times). It's common sense really.
Bringing Force of Nature back in the game would solve a lot of these issues. If you think 76 Magic Resist is too high of a value then reduce it to 70. The problem is that currently there are no ways to itemize vs. heavy magic dps, only burst damage. Bringing in a high MR, high regen, no HP item would solve a lot of these issues
Flat damage reduction via Doran's Shield does that - flat reductions hit fast and low damage much harder than slow and big.
Still: with counter-itemization you run into the issue where only certain champions want certain items, which can cause more problems than solutions.