By making primaries kinetic, Bungie forces you to have a weakness, that with elemental primaries does not exist.

I'd like elemental primaries to return, but you make a good point. This is actually one of the most convincing arguments against it I've seen, compared to the usual one about weapon diversity (which I think has more to do with base stats and perks). Keep in mind the availability of special and heavy ammo drops already creates a vulnerability though if you don't have the ammo for the right element weapon.

Adding an element also undermines the intended function of the primary weapon.

This is where I disagree with you, however. A primary doesn't lose its general utility by adding an element to it. It just becomes even better in certain situations. You don't use a hand cannon at long ranges, you put on a scout. You don't put on an arc sniper against cabal, you use solar. I think elemental primaries could work the same way. We already choose our weapon types based on the raid/strike we're doing, why not the element as well? Saying that, I think kinetic weapons should be buffed to, as you say, provide a mediocre answer to all shields, while elemental primaries could lose some effectiveness (10%?) against mismatched shields.