I've thought that "Crystal" should be named "Platinum" ever since the game came out. When I first heard there was going to be a third added on to G/S, I thought that it was going to be called Platinum, until the official name was announced. And then when I heard about Platinum I thought, "Well, NOW they use it..."
From an in-game perspective, though, I guess it makes more sense that Crystal is Crystal. The mascot Pokémon of that game was Suicune, which looks more like crystal than like platinum.
And while crystals, diamonds, and pearls have more in common with each other than platinum, diamonds, and pearls, logically it wouldn't make sense for Crystal to be the upgraded-and-better-than-ever Diamond/Pearl. Diamonds and pearls both are a lot more valuable than crystals are, so based on the names you'd think the game would be less valuable than either of the originals. (They might be worth more than platinum too, but I don't exactly know the "conversion rate" between diamonds, pearls, and platinum. :P) If Crystal were part of the Gen IV trilogy, it would make more sense for the games to be Crystal/Pearl/Diamond or Pearl/Crystal/Diamond than for the games to be Diamond/Pearl/Crystal.
Then again, crystal probably isn't worth more than gold, either. Ehn.