Here are three tips to decrease the annoyance of looting people, animals, and plants:
You automatically loot any body you pick up. I don't think this requires a skill, but I didn't notice until about a third of the way through the game.
As stated in the comments, the Loot Takedown skill allows you to loot any enemy simply by performing a takedown--even. While the skill says it works for all takedowns, those performed at a distance with the skills for performing knife(knife, pistol, and grenade at least) don't seem to apply. I haven't paid enough attention to vehicle takedowns because they're just too much fun. \o/
Hold the interaction key as you run up to dead people, animals, and plants to minimize the chance of accidentally switching weapons. Make sure to look down at the object and stop over it (seems to help for bodies). It's not fool-proof with peoplefor avoiding weapon swaps, but it works about 95% of the time for me.