I thought the plot of the Mega Man X series became more interesting in X5 and X6, although a large chunk of the plot for X6 was lost due to the worst Japanese to English translation EVER. There were massive hints in these games that Dr.Wily was somehow still pulling the strings, even though he was supposed to be long dead (The "W" forming behind the Shadow Devil, Sigma talking about an "old man" who hates X and created Zero, Isoc in X6 being able to completely neutralize Zero). I was fully expecting some great revelation in X7 or X8, yet Capcom decided to focus on introducing Axl and the New Generation Reploids.

So yeah, I agree, the Mega Man X series definitely could have used some better writing.