Man that was hard to get.
I've been reading through the whole post, and I have to mention some bullet points about Moody, but first I want to talk about the main users of this ability, which are 4 (Bibarel, Glalie, Octillery, and Smeragle)
General Comments
-All of the 4 users of the ability, are weak to Aura Sphere.
-Moody, when one uses it, you never ever get the evasion or speed boost. When the rival uses it, he always gets it.
Bibarel and Octillery
-Both are supposed to work the same way, the only difference being: Bibarel goes physical, while Octillery goes special. Their only coverage are Return and Waterfall for the former, and Surf and Ice beam for the latter. The other two moves are Protect and Substitute of course. (Surf and Waterfall are boosted by rain btw)
-One can work around it, and eventually take them down, but that basically depends on the boost those Pokemon get. If they get evasion, or speed, and if you lack an Aura Sphere/Thunder user, then gg. However, as mentioned before that's a 2/7 probability.
-If there are Toxic Spikes up, then that might a problem, because while the Moody Pokemon are getting their boosts, the rival Pokemon is losing HP every turn.
Glalie
-Same story as for Bibarel and Octillery, with the difference being coverage moves, and lack of boost under weather.
*However, we got one of the most annoying Pokes to get this ability:
Smeargle
-He can do pretty much everything you want. Spore and Protect are two moves you will always see from this lil' guy. The other two moves? They could be Batton Pass, Substitute, Taunt, Mirror Coat, Stored Power, Ingrain, Double Team, Shell Smash, Quiver Dance, bla bla.
-Spore + Protect means that he can get at least 3 turns of Moody, so the likehood of getting an evasion or speed bost increases. From then, it can do pretty much everything.
Personally, during my journey on the ladder, I've faced at least 20 Moody teams. I lost to one guy, due to Evasion and Speed boosts, and after I lost he PM'd me asking for some advice on the team he had. I used some terms such as "Metagame" or "Revenge Killer" and he asked: "What is metagame and revenge killer?". I felt terrible for a while.
The point is, some unexperienced trainers may get the luck on their side and turn the tables in 2 or 3 turns where they can set up and proceed to win. This brings the concept of luck to the game, which has been greatly discused. One can even make a standard team with like 3-4 pokes and the last guys will be a Moody user, and then see how it goes in order to beat you up. I know luck may be against them, but it may not be against them either.
Anyways, I think Moody should be banned.. I can't say forever because next Gen GameFreak might think about making it raise +1 and drop -1, or who knows what... but at least during 5th gen, I'd say it must be banned.