I'm slightly confused by your question. Your title seems to imply that people are critical about Square Enix as a whole, but your post suggests a focus on criticism of post-Squaresoft Final Fantasy titles. So I'll address the second part.

I think there are several reasons why a lot of people have become critical of the Final Fantasy series under Square Enix. One of the main ones is that that it takes Square Enix too long to develop Final Fantasy titles, which I think is probably one of the worst complaints I see about the series. It makes me wonder if the person asking this question is stuck living in 1999 when game development was much simpler and less expensive than it is today. Modern AAA titles take far more resources and development time to create compared to when they did in the Squaresoft days. I wish we could go back to the old days of 1997-2002 when we had five mainline Final Fantasy titles release consecutively, but unfortunately it just isn't possible anymore. In saying that, I don't think it's fair to criticize Square Enix for this. Time goes on, game development becomes more complex, and video games get harder and more expensive to produce. Those are just the realities of the business.