The way I've got my loadout is if the soldier is carrying a weapon that's not good for close-range engagements (sniper rifle, grenade/rocket launcher, etc) they get a sidearm. For weapons like the GL that need both hands to fire but only one to carry they get the machine pistol so that they can simply draw, fire, holster since the MP is one-handed. Big weapons that need both hands to carry (like the RL) are paired with the SMG -- if they have to drop their primary weapon, they might as well get the best secondary, and its two-handedness doesn't matter in that case.
Obviously, I'm still playing with earth tech, otherwise I'd be trying the plasma pistol out.