Nah, I don't think Alita's gone sour. Basically, they've had moments where you doubt it, just like you initially did, and then a couple issues down, it'll all make sense and completely fit in with the rest of the series. This seems to be happening frequently throughout all I've read. Its like... the series will do something completely off the wall, and then recover over and over again, and do it to the point that, in hindsight, makes that stuff look good and fun to read through again. My question is, is Kishiro doing it deliberately? Or has he gone insane and has no idea what he's doing, yet somehow maintains such a degree of intuitive genius that he keeps it going despite his madness?
Negima!'s having some trouble, if you ask me, but nothing that it still can't fix. Right now its going through a rough spot where I think Ken's torn between what his fans want it to be, and he's trying to satisfy everyone. My hope is that once he's satiated his romcom fans, and the movie's been released, he can get back to his original story, and take his time wrapping it up. And yeah, I think we're not too much further from the end of Negima! now.
As for One Piece, that certainly helps, that it keeps the challenges interesting, but I don't think that's it. Look at Bleach. Bleach is constantly making the characters into wusses over and over again with stronger and stronger adversaries, no matter how far the characters have actually come. One Piece has taken a long time to establish just what the crews place in the world is, and they've had to work up from there. Which kind of mirrors Bleach. Adversaries have remained hidden, and the threats have increased until we've now gotten to a point where we believe what the overall standing is. So why is that One Piece works, and Bleach (in my opinion) doesn't? I come back to my previous case. Bleach forgot what it was about. One Piece hasn't. No matter what adversaries have appeared, no matter how the straw hats place in the world has been impacted, the series has remained true to the core constructed in the very beginning when Luffy was first putting together his crew. One Piece never got lost in the expansion of its narrative or its setting. Its always been One Piece, through and through.