1. Give BM hunters a 'Kill Command' style shot.
Meaning, give BM hunters a ranged attack that does the same damage, has the same base scaling, and has the same requirements (40 focus, active pet that is alive/in combat). Make them share a cooldown, so if you use the shot, you are locked out of KC for 6 seconds - likewise, if you use KC, you're locked out of using the shot.
Kill Command is not a shot. Its a nuke, for sure, but its a melee nuke. The problem with it being a melee nuke is that anything which disrupts the pet being within melee range = my spec can't use its most powerful attack. So for fights with air phases, or a lot of switching where KCing is a pain, you could use the shot. For fights without those nuisances, use KC.
The more simple version would be to just give KC a greater range, so that it can hit targets in the air/further from the pet, but I think my solution is more fun in the sense that it gives BM hunters something they have asked for (a true 'signature' shot) and helps with the major issue of losing dps to the above-mentioned factors.
2. Provide the spec with a Sword and Board-type proc.
E.G. something like "Your Kill Command ability has a 30% chance to make your next Arcane Shot cost 0 focus/deal increased damage/etc." Procs are fun when they don't rule the spec (see Ret paladins), and imho make for a more reactive, engaging playstyle. Giving BM a proc would only help the spec - both with dps and with the stigma that BM is the 'lolsimple' way to play a hunter.
3. Make pets immune to PvE mechanics like knockbacks, tornadoes, etc.
I can recall countless times while leveling/playing my hunter in Cataclysm where my pet was simply dead weight - Rahj in Halls of Origination, Altairus in Vortex Pinnacle, etc etc. These fights - and others - consistently handicapped my pet. While some might argue LOLDUNGEONS DON'T MATTER (an argument that is probably true to some extent), its not the dungeons I take issue with, but the near-complete disabling of my pet in PvE situations.
Pet AI is pretty simplistic, which Blizz themselves have admitted. So, punishing players for that (when it is in fact Blizz's fault) is not only annoying, its senseless.
I really don't think MOAR DAMAGE MOAR AP is the answer for BM because that only makes it more dangerous in PvP (where it is plenty lethal already) and inevitable for nerfing. I think it really boils down to improving the mechanics of the spec so that it can function with the same sense of 'uptime' as Marks and Surv.
As always, thanks for reading. :)