Another issue with phase ships is that while the cloak is great for dodging missiles, it doesn't get rid of them: not a problem with rockets/torpedoes, but the inability to get rid of harpoons and salamanders is a major issue. That isn't too bad of a con for small ships like the Shade, but when you need to dodge missiles with the Doom, it's no fun: you often have to generate more flux while phased than you otherwise would by absorbing the missiles with a shield-equipped ship.
An easy way to take incoming missiles that your point defense won't be able to handle, with a shielded ship, is to just hold fire for a second or two shortly before the missiles hit, passively venting flux to create a "flux buffer." Then, raise shields right before the missiles impact to absorb them.