From judging their lore and their army strength, I'd have to say the:
1. Hive
2. Vex
3. Cabal
4. Fallen
I think the Hive are first because of their close ties to The Darkness, but also their forces in general. Although the Vex are a close second, I don't think the Vex can compete with Wizards and melee Knights. Let's not forget Ogres. The Vex can travel time and whatnot, but they aren't that advanced and let's face it, they haven't killed us or won (yet?).
The Cabal have lots of firepower, and out in the open, probably could out slug the other 3, even though they lack snipers like the Vex and Fallen. Goliath tanks and Interceptors would end any of that, though. Plus, from what I understand they use planets as weapons.
The Fallen seem to be on the lower rung of danger in my opinion. They have speed from their Pikes, and have stealth, but even with the Archon Priest being a beast, I think they're the weakest army overall. Thoughts and feedback?
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Most annoying enemy in the game (IMHO) is a Vex Axis Minotaur. No weak spots, super strong shielding, and will teleport repeatedly to get right up in your face. If you can't nail it with a rocket you're going to have a hell of a time. Runners up would be hive wizards, cabal phalanxes and the Fallen stealth vandals.
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Vex are in theory, the biggest badasses in the solar system. Some of their troops don't even have weak points and blowing their heads off only pisses them off. Plus hobgoblins have line rifles. With incredible range and damage, it's pretty much the vex mythoclast.
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The Hive Wizards! God I just hate those things with a white hot rage!
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Humans