I like it, although I'm thinking that the water could do with some extra effect. I thought the light rays were pretty cool, subtle enough, not too overpowering.
But back to the water...
How about adding a little sparkle here and there, maybe with a particle effect of the sparkle fading in and out quite quickly. I think that would make the water more organic, people might pay more attention to the little sparkles than the repeating nature.
I'm guessing your drawing the water first, then alpha tiles on top for grass - so you could layer your effects as well. Like rain, imagine having some fog roll over the map, but have little splashes when rain hits the ground (or rather, random locations for particles). And when the rain hits the water, have a particle effect of expanding circles, I think that would look immensely cool.
The main thing about the water though, is that if your layering it like I think, then you could go totally mad with it. What I might try, is having a really dark base water, instead of the light water, I'd have dark blue drawn first. Then I'd draw sand or any terrain under the water, then the light water on top of that, but with fading tiles like with the grass. So, the dark water would make it appear deeper in the middle, because the light water would make it fade into the shore. But having the light water on top of sand etc would let you have under water things. I like to add in some wildlife where I can, so I would add in some carp, or some sort of fishies to swim around inbetween layers.
It can be tricky to do, but I think the game would benefit from some ambient colouring, like have it change the diffuse colours to suit the weather and time of day - most top down games don't bother with this, but I think more people should push the envelope. Would be really nice to be able to change the diffuse colour of each corner of a tile, but I'm sure that a global ambient colour based on weather and time of day would work great.

Health, Ammo, and bacon and eggs!
