I've added the default width & height values to the .nxmo file as specified, as well as vertical resize and nine-slice values.
This looks somewhat better than simply resizing the original version, but there is really no way to get around the "bubbles spontenaeously appearing in the middle of the graphic" thing, even with nine-slicing. However, I'd suggest that it's not really an issue, since that's what currently happens when layering/stacking multiple water objects manually anyway; i.e. the resizable water manifests the exact same result as manual stacking, which may well be perfectly OK, in which case - no problem.
However however, when actually stacking water manually it is possible to flip every other water graphic to avoid the "two distinct lines of bubbles" thing...
I suppose that, if creators prefer, they can still manually stack the water graphic at its default size*. But, those who would prefer the convenience of an automatic resize can do so, albeit with that much less control over the resulting image.
I've attached water.png, .nxmo and a demo level. Let me know your thoughts before I go ahead with the others; they will likely be a fair bit more work than the default one so I'd rather see what everyone thinks first.
*question regarding this: if vertical resize is not applied to a water object in the editor, does it appear as its specified default size in the editor, or the size of 1 frame of the graphic? Either way, I'd suggest that it needs to appear in the editor exactly as it will appear in-game.