The problems that Lactose lists are well known to most high end Hunters, and many of us mentioned them in the recent feedback request posts on the class forums, but Lactose and Cheeky have managed to sum them in an easy to read and understand list, like so:
1. It's possible to delay Auto Shots while using other abilities.
2. Steady Shot has constant cast time regardless of weapon, while Auto Shot has a variable cast time.
3. Highly susceptible to latency/frame rate issues.
4. Haste greatly enhances other problems.
In short, since Auto Shot can be "clipped" or pushed back by other abilities such as Arcane Shot or Steady Shot if they are used within its invisible 0.5 second cast time, you have to time the special abilities to go off perfectly in between auto shot cast times, while leaving as little downtime as possible so that you're shooting off a steady stream of DPS.
However, since Autoshot's speed can change so easily due to class-specific speed boosts like Rapid Fire and Improved Aspect of the Hawk or outside influences like Heroism or Drums of Battle, you may have to change your shot rotation in midstream to account for your new weapon speed.
Of course, you also want to make sure your total haste rating and base weapon speed is optimal for your shot weaving choices. In the case of Beastmasters, this means a Karazhan gun, the Wolfslayer Sniper Rifle, will end up being arguably better than most Tier 5 ranged weapon drops, and the Crossbow of Relentless Strikes will probably be better for them than the Black Bow of the Betrayer. It also means that all that haste rating that seems to be going on new gear lately can turn out to be a liability if it throws off your Auto Shot speed and makes it harder to properly weave in shots.
Finally, you also have to worry about your connection's latency. If it takes you a split second longer to send information to the game, you can start clipping Auto Shots when you tell the game to fire off a Steady Shot, meaning that your optimal 1.7 Auto Shot speed suddenly needs to be 1.9 to account for your latency. All in all, it's a major balancing act that to go through, and one that feels like it needs to be simpler.
With Lactose's version of the post (Seriously, you should read it) getting some love from Vaneras, we can only hope this means good things for Hunters in the future. I know many of us would love to have a DPS method that does not involve careful balancing of weapon speed and haste and an almost mandatory need for a super-fast internet connection. Perhaps in WoTLK, We'll see another change?