It's generally a very bad idea to place game control mechanics on a curve. There's a reason that action game characters don't slow down at low health. Having your control set change is a horrible feeling and ruins the intuition of controlling your character.
Ah, I have a feeling my point wasn't clear. It's this: if phase ships can be hit with enough EMP weapons for these mechanics to come into play, this means they're already easy enough to hit and these mechanics aren't necessary for making them easier to hit.
Subsystems can be shut down by more than just EMP, a good whack will shut them down as well. That moment of vulnerability is rare, but would still drastically change phase play. Phase frigates would be forced to disengage, not a problem against cruisers but a struggle against other frigates. The DOOM has too many redundancies to get totally shut down, so it's not an instant death sentence for them.
I still think that phase subsystems is the right way to go. It's very dynamic and creates more exciting situations for phase ships. Subsystem mechanics mean that a phase ship taking constant chip damage is going to have a malfunction sooner or later, and then the hunter becomes the hunted. The challenge is simply finding the right sort of punishment for it. For example, what if the ship can still phase but it loses mobility under cloak? The phase ship is effectively trapped, burning flux but unable to truly escape. Should it stand its ground or try to escape in normal space? Does it have enough flux to do the repairs in cloak? That's a complex situation and I don't think players can really intuit how it will work unless they play it.
