SR tries every single edition to completely rework the Matrix rules and make them fun. It never worked, but the issue surely was recognized.

As for mages, only astral projection is an issue. Personally i would get rd of it altogether as it is too powerful as well as it is not plausible for most antagonists to have a proper defense against it. Astral perception is good enough

But niche protection ? Nearly every single SR character i know is a hybrid and i have seen and even played every single common role as part of a hybrid. The system itself does not force niche protection all that much. It's all expectations and tropes.