I like the Raven Chaser a whole lot better than the Lost Ship in the Sky...mostly because it had the BO in it. There were too many plot holes in the Raven Chaser though, like: "Where did Shinichi go?" "Why in the world did a little kid make an entire deduction?" "What happened to the helicopter?" "Why was the helicopter shooting at the tower?" "What happened to the body?" "Why in the world would anyone choose to disguise as Yamamura keibu?" "Why was the hard drive/USB/whatever-it-was shot through?" Too many questions, partially why I like Fallout which attempts to answer most of those. Even the Organization can't clean up all that before the police arrive and the crime scene gets on national television.
As for the Lost Ship in the Sky...I didn't have too much of an opinion on it. A bit lame and not much of a true plot. I mean...rob a highly guarded facility just so you can steal statues to sell in the underground market? Isn't there anything better you can think of?
Off Topic: I can't wait to see Quarter of Silence though...I heard the plot is much better and more realistic.