I agree with Niwantaw's original statement that both armor and shields should be viable. They should also be distinct, so that a ship with 5,000 points armor and 5,000 points shield is protected differently and moves differently than a ship with 10,000 points one or the other.
Different weapons should definitively affect them differently, and I think maybe "energy vs kinetic" was just one way of showing that. However the devs mix it up will be awesome, and I'm pretty sure they'll mix it up.