OK, let's see the best options for each tier :
Common : Mantis
Uncommon : Mattock
Rare : Arc pistol
Ultra-rares : Wraith or Talon
Conclusion : SMGs suck no category of weapons seems to dominate so much, according to this fast but admiteddly very imperfect way of assessing weapons. The ranking would perhaps change if I picked the two best weapons of each tier... what I couldn't do actually since there's is only one uncommon pistol and one uncommon SMG. I'm not sure which methodology we could use to determine rigourously the best category of weapons, if there is one.
I feel that the ability of shotguns to bypass the shield gate was inevitable, because the short / mid range fighting they impose needed that kind of reward. Besides, not being able to one shot kill infantry units like Centurions or Marauders with a shotgun would be too frustrating... and would not fit with the big boom they produce. At the beginning of the game, this property of bypassing the shield gate made shotguns the prefered weapons even for infiltrators with a sniper rifle damage bonus at rank 6 of Tactical Cloak. Then Bioware introduced phasic rounds, and kinda rebalanced things.
I agree with Slasher that shotguns are the most popular here, but IMO it's not because the category is inherently broken but more because
1) they're the most fun
2) They're very varied
3) regarding killing efficiency, this game is best played at short / mid range most of the time. This is due to the presence of powers allowing to close distance, to the existence of RHA, the design of the maps (not so many long lines of sight without cover) and of the enemies (not so many units that can snipe you). These characteristics allow experienced players to safely rush circularly from spawn to spawn. In this situation, having a shotgun in hand is often the best solution.