See what the dealer is willing to do first. If they're worth their salt, a good dealer will be willing to exchange it, and a really first-rate dealer may perhaps even cherry-pick one for you, based on what you (politely) tell them you're hoping to see in the fit/finish of the knife. If they're not helpful at all, I'd avoid purchasing from them in the future, and make sure they know why. Then see if Case is at least willing to fix the centering issues (they do this all the time). With the coloring issues of the bone covers, they're more likely to just send you a replacement anyway. In this event, a two-birds-for-one-stone solution (blade centering + color issues) may be the best option anyway.
The 'natural' character of bone will usually mean one bone cover won't necessarily absorb dye/stain as readily as another, which accounts for the light-to-darker variability seen in the color. Case has a very long history of making bone-handled knives with noticeable variation in the bone covers (Ed's example above is a perfect look at that). I've never viewed it as a defect, personally, and I like the character added by it. To me, it's a more sure-fire indication that the 'bone' is actually real.
David