I'm torn on his live action films. I think they're all great, but flawed films. Which is partly why I love them. They're like your annoying kids who surprise you and disapoint you while still clearly being your own kids.
Royal Tenebaums (most cohesive, even with it's sprawling cast--grounded in a way that makes the movie electric. But, the opening 20 min or so is a little overlong.)
Bottle Rocket (Wes Anderson clearly still cutting his teeth as a director, but his characters feel energetic in a way he doesn't always let them be. The weight of childhood friendships pulls this one up high, for me)
Fantastic Mr. Fox
Grand Budapest Hotel (Wonderful, but slight. The underdeveloped relationship between Zero and the Baker Girl lessons the impact of some late-game developments.)
Darjeeling Ltd. (Strange, structurally--with the 15 min prologue and the flash backs to the funeral. Maybe Wes' most emotional film, for all of it's stunted emotion.)
The Life Aquatic (Would be higher if Steve just wasn't so incredibly hateable. He brings his own movie down by being too terrible, at times. His son's death (or not?) leads to one of the greatest moments Wes has ever filmed, but every time, on reflection, I wish it was tied to a character who wasn't quite so despicable.)
Rushmore (Similar to TLA, but the lengths he goes to make an ass of himself make it hard for me to rewatch. Steve Z. is at least a pathetic old man with few shits to give. This kid is so young to be so self-defeating, it's painful).
Moonrise Kingdom (Probably Wes's most rewatchable live-action film, aside from Grand Budapest, but I find myself wishing the film spent more time with the adults--probably not the film's goal.)