The plasma pistol is better for taking down the shields of individual enemies. If one or two brutes are fighting you, plasma pistol works the best.
The plasma rifle is better for taking on multiple shielded enemies, preferably in a tight group. If there are 3 brutes, a brute captain, and 2 jackals, you want a plasma rifle handy. It's also more effective against grunts and drones that may interfere while you're taking down enemy shields.