Heavy Plasma vs Sonic Cannon
Lacking auto fire and the massive clip of its ancestor, the Sonic Cannon nonetheless stands out as a useful weapon. The inhuman power of the weapon allows its use against all but the toughest aliens. While the clip is small, the damage per shot more than makes up for it, and the accuracy is highest of any weapon in the game. If only firing wasn't so much slower.
Where it really falls down is base defense. The smaller clip, lack of auto fire, and high TU cost of firing unfortunately make the Sonic Cannon much less suitable for garrison use than the Heavy Plasma if one uses less-than-stellar troops for base defense. The way the math works out, with the values chosen for weapon accuracy, a three-round burst generally has a higher chance of getting at least one hit than a single aimed shot. To counter this deficiency, the Sonic Cannon user should carry a suitable close range weapon.