Problem: Silencing Shot is too powerful for PvP
Solution: Remove Silencing Shot. Yeah. That's right. Make hunters the only dps class (and practically only class/role) that doesn't have an interrupt. Instead make it the hunter's own. Give hunter pets the ability to Skull Bash. Make it just like the feral druids get. This is good because it will make PvP opponents deal with the pet with interesting counters and it keeps PvE alive.
Problem: Level 30 Talents
Solution: That tier is all about CC now and always has been. Pull Binding Shot out of MM and put it there with Wyvern Sting and Intimidation. It's simple and it doesn't give MM an extra form of CC.
Problem: Stampede is too powerful for PvP but hits like a wet noodle and has no utility now
Solution: Since a hotfix during 5.3, Stampede no longer allows pets special abilities, buffs, or special attacks to fire in Stampede form. This is poor for Brawler's Guild, Challenge modes, Arenas, and other small group activities. The DPS nerf is quite significant as well. Keep this utility and DPS nerf. Instead give Hunters a reason to hit the button: During the thundering confusion of a Stampede, all damage is reduced by 20% within 30 yards of the pack.
Problem: Readiness is too powerful in PvP
Solution: Hunters need a mechanism to burst DPS because that's what hunters are supposed to do. Readiness also gives hunters a great deal of flexibility to different situations. Bestial Wrath is already nerfed. Lynx Rush and Stampede are nerfed. Leave readiness alone.
Problem: Arcane Shot is becoming way too big a shot
Solution: Do not further buff Arcane Shot. Soon hunters wont bother using their "signature shots". Instead, increase the damage of those signature shots!
I've reposted this over in the PTR thread. Feel free to sign in there and up-arrow if you like it.