The most recent M. Night Shyamalan film I've seen is The Village (which I really liked, by the way), so I'm not really qualified to say that all of his films are good, but I do get the impression that most people don't give them a fair chance. It seems like people see his name and think "twist at the end..." without really actually wondering if maybe the film itself is good (whether there actually is a twist or not).
I liked The Phantom Menacé too. I was, like, 9 at the time. I probably just wasn't paying attention to much of it. If I had it on DVD or something I'd definitely check, though.
On the popular-things-I-dislike side...
There were some bits I didn't like in Avatar. I've only seen it once, and that was almost a year ago so I don't remember it clearly enough to really say whether or not I like it overall (I definitely liked it at the time, though). What I didn't like was all the montages of the guy learning how to do stuff. "And then, this happened!" is not good film-storytelling in my opinion. I get that, in the story, it was necessary for him to learn those things, and that if the film included the entire learning process it would probably be quite a bit longer, but it just kind of feels... jumpy. I don't know why, but I feel like that sort of thing works better in books. Maybe it's because books uncontrollably have narration, narration that is (usually) neither a character from the story nor has any personal involvement with it. When there's a narrator in a movie, it's usually one of those things, and I feel like it doesn't work as well when we have someone telling us what they did, rather than kind of matter-of-fact type statements. I don't really know for sure. I don't completely understand this dislike.
I can't think of a popular film that I actually full-on disliked. There might've been some...