Well, one person not seeing the need for a particular feature doesn't mean no one would want that feature. And so it's often in a tileset maker's best interests to implement a variety of a features, whether it's a standard feature or not. Still, no one's forcing anyone to do anything they don't want to.

The reason Mystic Isles 2's water doesn't look as great as it could be is because water often times uses gradients other than those used for the textured background. It's a similar issue to translucent tiles and how other tiles look underneath them. Judging from Mystic Isle's palette, it might've been relatively easy to add extra gradients just for making the water look better. From what I can tell, the more complete gradients a set uses, the more likely the water will look good. Incidently, having a palette composed entirely of gradients can make it easier to create different versions of the same set, which is always a plus (I might've felt more compelled to use Mystic Isles again if it came with an evening and/or night version).

My comment wasn't meant to imply all new tilesets should have water that works in 8-bit (although that wouldn't be a bad thing). It's to say that if you have the tools and the knowledge, might as well at least try, and even if you can't get it right, it's probably not going to be the deciding factor of whether or not your set gets used.