Sfx might be nice, but consider making it a little quiter or add setting for it. As a gamedeveloper and video editor I can recommend something around -18 db and lower to not steal plfyer's attention.
About a fix for shooting enemies. I'm not working with Unity, but I know that it has good and simple system of collision layers. Just google it and you'll be able to fix this problem in a few minutes.
To make your game intuitive you need a very good idea and whole group of playtesters to setup a feedback loop. And even with all of this, you won't be able to make game intutive if it has some level of complexity.