Non-linearity in E4 is a good thing for me. Obviously that wouldnt work for gym leaders but E4 is supposed to be beaten at the same time. Why it's a good thing? I think it does the difficulty right in a way, that you have to be prepared to face every possible combination of pokemon and you wouldnt lose just because one guy has higher levels than the other one. It was done in a wrong way in XY because it was way too easy.