Easily the Fallen. They've had their houses torn apart by one of their own kind in Skolas and when they almost had a united army it all fell apart. The only house that is even close to fighting shape are the Kings but we know so little about them it's hard to gauge them. The Hive lost an important figure sure but it's like one of our armies losing a lieutenant. Not really much of a loss in terms of leadership. Atheon was definitely a major piece of the Vex but there are a few theories about how he factored in to the Vex that make me think he wasn't so important to the Axis Mind. In fact, he may very well have been an enemy of those that worship the Dark Heart. If you want I could explain some of it, it's pretty interesting to think about. As you said, the Cabal have faced the fewest losses. I'm not really sure what sort of state their army is in. I think we'll get a bit more info on them once the Taken King drops