I actually feel like the old system makes more sense. The way I see it, there isn't a whole lot of gradual variation in armour protection. Any given shot is either going to hit a weak point or a strong point. The weak points in a given suit of power armour or whatever are all going to be about the same durability, and the strong points are all going to be about the same durability. Most weapons are going to be either capable of punching through the strong sections or they aren't. If they can, it doesn't matter where they hit, they're going through. If they can't, it doesn't really matter how close it is to being able to, it goes through if it hits a weak point, and gets stopped if it hits a strong section.
For the modifier system to make sense, all the heavier types of armour have to have a more or less even distribution of different thickness/strength sections. 66% of a suit of Power Armour can stop a Lasgun blast, but only 50% is strong enough to resist a Heavy Bolter round, 33% is durable enough to take a Krak Missile, and only 16% can handle a Lascannon shot. Where I can really see an argument for some form of modifier is with things like Blasts and Flamers, that are hitting most or all of any given target if they land at all. Even that feels more like it should be maybe a "re-roll successful saves" thing rather than a linear modifier, tho.
I can see pros and cons to both from a rules/game balance point of view, but the all or nothing system definitely feels more "right" to me.