Wait.... starting choices? What do you mean by that? Do you mean items that are appearing in the room you start in? That shouldnt be happening, if that's the case.
As for the Guardian Gun, I'm not entirely sure what it's intent is. This type of game being what it is, there are going to be a few items that are meant to be "super items" in that they're incredibly powerful and perhaps even OP; it tends to be a fun thing when games like this do that, particularly since it doesnt REALLY break the game since every run can be so different.