From last year's fiasco, it did seem like the actual toys being stocked were completely random by store.
Shipments come every 5 days:
Toys 1 & 2: Pinkie Pie and Rarity (By March 5th)
Toys 3 & 4: Twilight Sparkle and Fluttershy (By March 5th)
Toys 5 & 6: Applejack and Lily Blossom (By March 10th)
Toys 7 & 8: Rainbow Dash and Cheerilee (By March 15th)
This can vary store by store, but this is what they currently have set up. Each pair of ponies will most likely only arrive once per store, so it's best to check back often, and on the dates they should arrive.