For marksman type weapons I believe I would choose the Spec Ops BR. It really helps in missions like AOTCR, picking off those jackal patrols without waking the sleeping grunts up, though normally use Particle Carbines for its massive damage against energy shield systems (perfect against Covenant).
Towards the later end where auto-fire and heavy firepower became more important, I would pick the Brute Plasma Rifle and Brute Plasma Pistol as my favourites. The Brute Plasma Pistol's overcharged shot, as you said, is pretty useful, laying down barrages of plasma against hordes of Flood. Pretty good against Covenant too. The Brute Plasma Rifle has pretty good accuracy and range even though it's auto-fire. What's more it is good against every type of enemy infantry, be it Elites, Brutes, Sentinels or Flood. To top that off, both Brute PP and Brute PR have a decent amount of availability.
Design wise, however, I would probably vote for the Shredder or the Piercer.