Behind cover does not mean 100% covered in game terms. It means you have a lesser chance of hitting them. Mechanically there are three levels of cover -- half cover, 3/4ths cover, and full cover. Only full cover means you can't be seen.
And Magic Missile can't hit Full cover either, but it's not because there's something in the way -- it's because the caster can't see the enemy so they can't target them. As long as the caster can see the target the Magic Missiles will always hit him. That is part of why it's such a useful spell.
This is what I'm advocating for. I'm not saying that you should be able to hit targets you can't see, but if you can hit an enemy with 1 missile, you should be able to land all of them.
The reason I brought the idea up, is because from a time and effort standpoint, it doesn't seem like it would require much of either. The paths are already in place, it would just be adding the functionality to choose which path each missile would take. It would also grant enough usability for the spell to function closer to its intended design.