Brilliant.

Ever the optimist, I hope there is a CSS solution to this.

Reasoning:
They only collide, when a mouse-user points on a focused link. at that point the user either knows that the link has focus (he saw it before hovering) or he doesnt care about it having focus. In contrast, all reasons for showing him a hover-effect to reflect his action still apply, since he obviously wants to click and not hit return to open the link.

The lvhfa argument “clicking a button is what I do with them right after I gave them focus” does not feel correct to me, since this “giving focus” is just a sideeffect of clicking/activating and not really user-intended (unlike with textfields), which will make the active:-rule instantly overwrite the focus:-rule anyway (if we stay with the example of just different colors).

The most transient pseudo-class is active. It applies only during the brief time the user holds down the mouse button. Therefore it is the last. As it lasts only a short time, it should override everything else.
The most permanent class is link. It applies to any link. Therefore, it cannot override anything else, it must be the first.
Visited is next after link. It doesn’t apply to all links, but it applies irregardless of current user activity; instead it depends on past user activity. Once visited applies, only time or a history purge will make it not apply.
So the question remains of the relative order of focus and hover. I’d say that the mouse, which causes hovering, is quicker-moving than the keyboard focus, so hover is the more transient state and is ordered later.

a:link {color: blue;}
a:visited {color: purple;}
a:hover {color: red;}
a:focus {color: orange;}
a:active {color: yellow;}

In other words, focus -for an anchor- fits between the active and hover states. The rationale is that I see ‘focus’ as something you do right before interacting with an element.
Thus, I give focus to a textbox before I can type in it, to a button before I can click it. Anchors seem to fit the same pattern. So, hover and focus feel like they should be related, and focus and active too, since typing in a textbox, or clicking a button is what I do with them right after I gave them focus.

At least that’s my story until I get more coffee.
F.O.R.