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I think a key difference is already in the names. In one game and world it is "hull", in the other it is "armour".
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For indeed, in the world and lore of Mechwarrior or Battletech, it makes sense to have directional armour. After all, armour has the one and only purpose to absorb damage from enemies. Mechs move on a planets surface, so with significally less degrees of freedom than in space. A mechwarrior can be expected to place and use his armour to prevent damage to internal systems. And indeed, in MWO one skill any good pilot has is to roll damage, to distribute it over the mech or absorb it with still well armoured sections, while protecting those parts of the mech which already were damaged.
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So for MWo it is perfectly fine, i wouldn't have it any other way. But in contrast, in this game we're speaking of a spaceships hull. In terms of gameplay, the hull is there to absorb damage, and most often this damage again is hostile fire. But a shapceships hull is not designed to only absorb enemy fire. It is there to hold the ship together and protect it against anything, be it the stress of hyperspace or supercruise, be it heat and radiation when being too close to a star or also pressure and temperature differences when landing on a planet. (Sure, currently the game doesn't support landing on planets with atmosphere, but that's a matter of not being implemented yet. It is supposed to come in the future and within the games lore, where planets are settled, ther must also be a transportation to them, which is just not coded yet. )
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In conclusion, if a ships hull is supposed to protect against all these threats, instead of being there solely to absorb enemy fire, i would immediately sack any spaceship designer who leaves some parts of the ship with noticeably less protection than the rest of the ship. The two games have different ways of handling damage, and for each of them it actually is fine. They make sense based on the lore and what is being simulated.
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