Different enemy rats have different resist profiles, speeds, orbit distance etc. This means that some weapons are better for some missions than others. The same agent can give missions against different foes.
Same thing for PVP. Every enemy has their strengths and weaknesses. You use the right tool for the job. When you start you might focus on getting good at a weapon system and then pick targets accordingly. later on as you gain more skill training into different ships and weapons you have more options to take a wider variety of enemies.