I wouldn't say that mutants as endangered species ruins the X-men. I'd be more inclined to say that extinction stories that are poorly handled tend to ruin the X-men. What makes the Terrigen Mist story so egregious is that so much of it happened off-panel and the Inhumans came out with absolutely no ill effects. If there was a war, then the X-men definitely lost and for some reason, there was no sympathy whatsoever for them. Combine that with Marvel's unspoken agenda for undermining anything for which they don't have the movie rights and it's perfectly understandable why these stories would be so bad.
With respect to villain, I think that's a similar issue. It really depends on how the story is handled. An extinction story can bring about new villains, but only if the story is strong. Right now, Marvel doesn't seem to be committed to strong X-men stories. They don't seem to be committed to the X-men in general, at least not until the issue with the movie rights is resolved. It took years for the M-Day plot to play out. I imagine this plot with the T-mists will be even longer or until the movie rights issues are settled, whichever comes first.