Would you be upping the AV at the same time though? Otherwise I feel it would make power armour too vulnerable to the more powerful weapons

Precision attacks are unlikely to affect the effectiveness of the more powerful weapons. There'll be a to-hit penalty for precision attacks, so for weapons which already have a fair chance of breaching power armour anyway, trying to aim for weak spots will actually worsen their damage output.

For a rough example, let's say a precision attack is a -20 to-hit and gains Penetration(D6). If we have a BS 60 character (no other modifiers).

With a 2D6 autopistol:

Standard shot: 60% (hit chance) x 8.33% (rolling 11+ on 2D6) = 5% chance of causing at least one point of damage through AV10

Precision shot: 40% x 50% (rolling 11+ on 3D6) = 20% chance

With a 2D10+4 bolter:

Standard Shot: 60% x 85% (rolling 11+ on 2D10+4) = 51% chance

Precision Shot: 40% x 96.66% (rolling 11+ on 2D10+4+D6) = 38.66% chance

Those numbers may need balancing, but show that it's entirely possible to make precision shots so that they benefit low damage weapons, but not those weapons that already threaten power armour.

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That said, yes, introducing these options could possibly be used to justify toughening up some armours in IRE.

With precision attacks, power armour could actually be put up to something like AV12, yet still remain more feasible for low damage weapons to pierce (continuing the above example, a 2D6 autopistol would have about a 10.4% chance*).

* That's ignoring the chance of the target evading (they're more likely to evade a lower to-hit value). However, I've not yet looked at encumbrance in IRE. It'd be entirely possible to balance an increased AV for things like carapace or power armour with an evasion penalty** - wearing a quarter tonne of armour might be very good at stopping bullets, but you're not going to be dodging them.

The advantage to Astartes armour might then be not that it's thicker, but that the Black Carapace makes it much less encumbering.

** Also, I have currently included power armour with a mention in the target size modifier rules (wearing power armour does make you a bigger target). But I'll make it more specific when I get to that part of the Armoury.