For AL, Scouts, Infiltrate, Stealth, and Hit and Run seem to set them up as Strong Skirmishers and Saboteurs. Maybe some type of special weapon or rule that reflects their high cost-low model situation? Maybe something like the Hellions rule to be able to drag an IC out of CC after they make their Hit and Run move? This could be used to change the role of the Alpha Legion depending on what was used to move them, this being an example for the Cult of Hydra.
By using the Dark Apostles to move the AL, you could set them up to be fierce warriors, backed up by the fearless and preferred enemy USR's. Maybe an additional rule such as Rending could go here? Again, it sets them up as high point-low model strong fighters. Plus by changing the way you move AL, you change the role of Alpha Legion and the role of the entire army, leading to varied lists.
Have you considered an army-wide Preferred enemy against Loyalist Marines? Reasoning being many Chaos Marines still consider the war against the Imperium to still continue, and it represents their eternal hatred of the Imperium. Another reason could be that since they are essentially Space Marines (just totally evil) they know the weakness of how Space Marines fight and operate.
As far as Plasma Spam, I dont really have any idea's apart from making it insanely easy for models to access Plasma weaponry. Maybe letting Havoc's (I had a feeling calling them Dev's was wrong
) take Plasma Cannons?
I do agree with your reasoning on Tank Hunters though. Maybe you could enable to have different roles in the game by making various USR's able to be purchased for them. ie Melta Chosen w/ Tank Hunters, Sniper Chosen w/ Scout and Infiltrate etc. Although I do see this as perhaps making Chosen too overpowered...