The overwhelming majority of the tone a player gets comes from the player. As has been said above, to decide which you like you really need to play them. If you decide you don't like the sound of a sax, what you really mean is you don't like the sound you make through that sax.
First things first. Have you played another sax of proven quality? If so, I presume the intonation problems you have on the cheapy went away? Both the horns you mention have good intonation. No sax has perfect intonation, the player has to make it play in tune, but some are definitely better than others.
I've played both the the Yamaha and Yanagisawa, and I've owned a number of Yamahas and still own two Yanagisawas. The build quality on both is in my experience exceptional, and they stay in fine playable condition without the need for frequent technician intervention. They also both have excellent ergonomics. Personally I'd pick the Yanagisawa for its quality and feel. I've played loads of Yanagisawas and contrary to what David has said, I find them to be consistently good rather than variable.
I have read some of the internet stories about lacquer bleed on Yanagisawas. Neither of mine suffer from this problem, and I get the strong impression that a large part of it comes from an anti-Japanese bias exhibited in certain quarters of the web. It's all very reminiscent of the campaigns against Toyota cars in some areas. Think about it and make a rational decision, not one based on bias (which I don't think you have, given the two saxes you are considering).
What does it say about the quality of music from marching bands if it is acceptable to play a sax with poor intonation in one?
A final thought. Once you've got your new sax, the thing to do is just play it - that's how you get to be the best player you can. Agonising over which sax you should or should not have bought doesn't really help, once you're over a certain quality threshold, which both these saxes certainly are, neither will in any way impede your progress. Neither in themselves will advance your progress either, only you can do that. Personally, I have owned an awful lot of saxes, but that's purely because I trade in musical instruments as well as playing them. I also keep a couple of old ones for purely sentimental reason (old softy that I am). Other than that, for actual playing, it's one soprano, one tenor, one alto, one baritone, one c mel.