Rifles are the workhorse of militaries everywhere, but at the start your guys barely qualify as police. They're allowed handguns and cheap weak shotguns because Murica! (X-files is set in the US of A and we seem to be going for that vibe) But police don't generally have access to rifles or bigger guns. Ideally they should have Kevlar and smoke bombs or flashbangs at the start, but nobody thinks they're actually necessary or useful, and everything useful is delayed.
Given that we're going for an X-files/police procedural style in the early game, I think it makes sense that the handgun is king for so long.
Maybe this isn't the place to suggest this, but what about early missions where you have to find some item or evidence and get it back to the point of extraction before a certain turn passes, everything not on a green tile is lost, enemy reinforcements are inbound and you don't have the manpower or the mandate to do more. Thought of that due to the police procedural sentence. Alternately, if we ever get the ability to have reinforcements actually show up, a secure the location and defend against enemies coming at turn 15 or whatever could be fun. Still not the place for suggesting it, but whatever.