I own the Bent Graduate, because when it was time to buy this toy the Amethyst was out of stock. (Otherwise I would have gotten the Amethyst since it costs less.) I like the BG because it came with the nicest, plushest, cushiest toy pouch I have ever seen!
I recommend going with what color you like. I've heard rumors that the Bent Graduate doesn't come with the amazing pouch anymore (sadly), but I haven't bought one recently to find out if that's true.
They're pretty much the same toy (though being hand-blown, there will be slight differences with each individual toy). The Bent Graduate used to come with a really nice padded storage bag (mine did), but going by some more recent reviews it seems like they may not be including it anymore, which is disappointing.
As for color, mine is pink, but had the blue been available at the time I'd have gone with that instead. The pink's very pretty, but blue is my favorite color.
These are essentially the same toy. I'd make my choice based on price and color preference. I purchased the purple Amethyst because it was cheaper and it was the best color available at the time. I like both the blue and the navy blue versions, but not enough to purchase a second toy.
I like the color for the blue amythyst best, but the navy bent graduate is a close second - but comes with a padded pouch, where amythyst's pouch is not padded.. I plan to get the bent graduate.
This is something I have been trying to decide myself. I love the purple Amethyst, and the Navy Blue Bent Graduate. They are so close that I think what will decide it for me is the padded pouch. It is worth the few extra dollars to have such a nice place to store the toy. Don Wands has it; SSA Glass doesn't. I would wind up buying a pouch for the Amethyst, and that would be a higher cost than going with the Bent Graduate. So Bent Graduate it is!