Fiction absolutely matters. It produces and is produced by cultural norms. Scrutinizing popular texts tells us how society feels about certain things. The fact that mentally ill villains are a reoccurring trope tells us that mental illness viewed negatively. Again, TLS does not exist in a vacuum and it participates in this, intentionally or not.
Also, you don't know the intentions of the writers/director of X3 anymore than I do. You don't have access to their brains back then right now. But it doesn't matter. What we have is the text in front of us. If you don't think EVIDENCE matters, then there is no point to this conversation.
I also find it funny and telling that you act like I have impossibly high standards. Jean in TLS is a villain because she has a mental illness. That is different than a villain with mental illness. And where did I say no minorities couldn't be villains? Magneto is a jewish and he is a wonderful villain.
But in a world where mentally ill villains is a trope, why do we need any more?