Haha, no it is not just you :) I think with proper graphics, proper scale differences and using colors correctly (keep a set for friendly, one set for hostile) it should make it less confusing, at least to a shoot em up level of confusing! And sound! With sounds you could get a lot of help I think.

I have forked the project so working on a new game based on this and should be able to get it clearer.

Thanks for trying and feedback!