There are two separate issues. One was that some weapons were initially getting much higher dps than they should have for their ilevel (due to an issue with the way the ammo conversion was applied to some weapons). This problem was resolved within a day or two of 4.0.1 coming out.

The second issue is that shots affected by weapon damage are not normalized for speed, so slower weapons will contribute more damage to those shots. Previous to 4.0, steady shot was fully normalized for speed so although the other shots weren't completely (the AP portion was normalized but the weapon damage portion wasn't) it was less of a factor. There's been no indication by Blizzard that the consider the current implementation to be a bug or problematic (or any explanation as to why steady was de-normalized), so it's unclear if they'll address it at any point or if slow weapons will continue to dominate in the future.

Only this is not the case.
Apart from enh shamans (although I don't know how that changed after WotLK) all melee dps have their weapon normalized.
And it SHOULD be, because an instant special is totally independent on weapon speed. Faster weapons can't use instants more often than slower weapons.

The reason most classes still prefer that slower weapons is simply because of the average weapon damage.
Saying that shot damage shifted from weapon dps to weapon damage is a bit of mistake. The only thing that changed is that people simplified the formula, so it seems there is something different when there is not.

Basically the formula is as follow for normalized damage (normalized speed is 2.8):

Shot Damage = Weapon Damage + ( AP / 14 * 2.8 ) + ( AP * ShotAPModifier ) + Static Shot bonus

Now Weapon damage is a range, which is the main reason you see differences between individual shots; so for convenience sake we often go for average weapon damage. There are 2 ways to obtain this:
1. Average Weapon Damage = ( Min Damage + Max Damage ) / 2
2. Average Weapon Damage = Weapon DPS * Weapon Speed

Take number 2 and substitute that into the formula and you get:

Shot Damage = (Weapon DPS * Weapon Speed) + ( AP / 14 * 2.8 ) + ( AP * ShotAPModifier ) + Static Shot bonus

That's the normalized formula. Take the unnormalized formula and you get:

Shot Damage = (Weapon DPS * Weapon Speed) + ( AP / 14 * Weapon Speed ) + ( AP * ShotAPModifier ) + Static Shot bonus

Now you can simplify that (due to underlined common multipliers) to this:

Shot Damage = (Weapon DPS + (AP / 14)) * Weapon Speed + ( AP * ShotAPModifier ) + Static Shot bonus

In the end though you're still talking about a shot consisting of a summation of 4 factors:
1) Average Weapon Damage
2) General AP contribution
3) Shot dependent AP contribution
4) Static Shot bonus

Now 1 is part of the reason why even with normalized numbers people still prefer slower weapons for instants. Because that number will always be higher.

Nr 2 should ideally be normalized to make sure that the damage is consistent for all hunters. The only exceptions are when the actual ability can be increased or decreased depending on speed. Like auto attack (faster weapons attack more often); on next hit abilities (like the old heroic strike); speed dependent procs (like the old windfury; where faster procced more often but hit for less).
Keeping this normalized always gives you 20% of your RAP as bonus damage; getting this unnormalized however causes huge disparities.
For example the difference between a 2.8 weapon and a 3.0 weapon with 14000 RAP is 200 damage. That might not seem like much but that's an 7,14% increase from AP contribution just because you picked a slower weapon.
A disparity like that might cause a seemingly inferior slow weapon to outclass a superior fast weapon.

Number 3 is of course shot dependent; as is 4

It's definitely implemented that way. If you test aimed shot you can see the damage difference between the proc version and the slow cast version (you can also see the difference in the ingame tooltips). I really find it hard to believe it's intended though given the wording on Master Marksman says nothing about the proc aimed shot doing less damage. It may be something they put in for lower levels and forgot to adjust.

Well LW should be #1 along with JC according to my quick math just using weighted values at femaledwarf.com