None of the shots automatically pick a target anymore. You will have to manually target via clicking the mob or using tab. This is what fixes the bug where mobs were being automatically targeted if your current target died midway through a cobra or steady shot cast.
The hunter community on the forums has been pretty divided over this, with lots of QQ and name calling on both sides. I personally don't like the change as I nearly never had issues before, and found manually targeting mobs during an all out aoe phase to be a pain. There are macros that you can make that will allow you to emulate the old targeting system. I'm using this one:
#showtooltip Shot Name
/targetenemy [noexists, noharm,dead]
/stopmacro [noexists, noharm, dead]
/startattack
/cast Shot Name

Works like magic. If you have a cast sequence macro for aspect switching, you can put it in as the second to last line. At least that's where I have mine, it might be better someplace else.

Can you tell me the macro for aspect switching?

I have one that swaps between hawk and fox with steady/cobra shot (if I queue the spell before next cast it doesn't swap, but if not it swaps).

What I need is one that puts me into aspect of the hawk when I cast anything else, but doesn't take me out.

@Twill

This is the macro I have for my instant-cast shots:

#showtooltip Arcane Shot
/targetenemy [noexists, noharm, dead]
/stopmacro [noexists, noharm, dead]
/startattack
/castsequence reset=1 !Aspect of the Hawk, null
/cast Arcane Shot

The "/castsequence reset=1 !Aspect of the Hawk, null" is the part that ensures i'm in aspect of the hawk for all my instant shots. My cobra shot/fox macro is now:

#showtooltip Cobra Shot
/targetenemy [noexists, noharm, dead]
/stopmacro [noexists, noharm, dead]
/startattack
/castsequence reset=1 !Aspect of the Fox, null
/cast Cobra Shot

I have my "castsequence" shots on the #2 bar (the one you get when you click the down arrow of your main bar). My #1 bar has cobra shot without the cast sequence modifier. I primarily use the shot without the modifier and flip aspects when i need to manually, but in movement heavy fights, if i'm learning a new fight, or for pvp, i find the cast sequence macro to be invaluable.

Hope that helps!

PS - i'm pretty sure the exclamation point before the Aspect of the ______ is what keeps it from turning the aspect off once its on. I'm not a macro writing expert, i mostly just cobble them together with stuff i find on the internet.

I LOVE THIS.

Thanks!

Indeed the new targeting system in 4.1 feels like a significant nerf to hunter AoE due to the fact that having to select a target (which by the way may be already dead before you fire next shot) make hunters miss one or possibly more Multishots per AoE session.
I think the option Blizzard adopted is worse than any automatic targeting for hunter PvE content due to the fact that hunter cc involved(freezing trap mostly) is 1% of the action (0% on boss encounters) and DPS is 99% of the action. Unfortunately the later is dismissed to support the 1st. Considering the hunter's presence in PvP I would dare to say that even considering the issue overall, it is still a poor decision.
I do sincerily hope that in patch 4.2 they will implement a smart autotargeting system. something which upon death of current target selects closest target to the dead mob(not closest in front of the hunter) with priority on mobs with same name/type, uncced, in range of the hunter, and having autoshot stopped until next attack. If such a system still raises problems(PVP wise or for other reason), i think at least Multishot should aquire a target automatically if the previous one died.