613.3a. Layer 7a: Effects from characteristic-defining abilities that define power and/or toughness are applied.
613.3b. Layer 7b: Effects that set power and/or toughness to a specific number or value are applied.
613.3c. Layer 7c: Effects that modify power and/or toughness (but don't set power and/or toughness to a specific number or value) are applied.
613.3d. Layer 7d: Power and/or toughness changes from counters are applied.
613.3e. Layer 7e: Effects that switch a creature's power and toughness are applied.
Starting with a 1/3 creature, the effects are applied in this order:

Layer 7a - nothing
Layer 7b - nothing
Layer 7c - -0/-1 is applied -> it's a 1/2 creature
Layer 7d - nothing
Layer 7e - P/T switch is applied -> it's a 2/1 creature.

So (2) is correct.