I don't get it. They bypass shields a certain percentage of the time? How exactly is that helpful?
In the end, to destroy any ship you have to get rid of all the shields and hull points anyway (you aren't realistically going to kill the hull while the shield is still there, since the bypass percentage is so low, unless you were fully upgraded and shooting at a guardian or something). It just seems pointless.
And all the upgrades are to increase the bypass percentage, not damage. Doesn't that basically mean that the upgrades are pointless too, since they are only changing which hit points are taken first?
Furthermore, by hitting the hull and the shield simultaneously, you are allowing the repair and regeneration rates of the enemy ship to work together --effectively doubling their overall health regeneration for the period of time that they would have had full hull and you were focussing on shields. This seems like a bad idea to me.
Someone please explain it to me.
The only way I can imagine that this would be beneficial is if the game incorporated some sort of hull damage penalty, where ships systems lost effectiveness as they were hit. That would be cool, since a ship at half hull strength has probably taken some damage to it's systems too. This is not the case, of course. Even at 1 hit point, ships work at 100% ability, mobility, and firepower.