Then you have a very unrealistic game formula, unless the alines are protected by individual bubble shields. There is one universe which is similar to this game - Stargate SG-1/Atlantis. There you have several squads as the only line of defence against vastly superiour alien races such as the Goa'uld, Replicators, Wraith, Ori and so on... Yet, human weapons prove very effective to a certain point, like the real SMG P90c. Even with Earth based tech, they can effectively kill lots of aliens with superiour techology, without having any advantage. I'm only comparing things, I don't want to start a discussion about Stargate, but because the series are successful, I think the writers of that show have balanced things quite nicely.
During the episodes there are several creatures or constructs who are very resilient and almost indestructible, but they are an exception.
And only last thought about the real sniper rifle - you will get the sniper rifle from the start, but the sniper skill will need many missions to build up, in order to have a lethal sniper, or so I imagine this concept. And also, it doesn't have to be an old style sniper rifle... you get to upgrade it and such, be better in TU usage, better accuracy, etc.