If you want the best "straight from the camera" macros, you can't beat the "swivel bodied" Nikons. Although the 5400 compares quite well to other camera models, it doesn't really compete with the 950, 990, 995 or 4500 (swivel bodied models).
These models (950, 990, 995, 4500) can "fill the frame" with an object close to half the size of the 5400's ability, with lower distortion. In other words, you've got much better frame coverage (i.e., a smaller object occupies more of the frame) with the Swivel Bodied Models. They can fill the frame with an object of around 17-18mm across.
Checking multiple reviews, the 5400 seems to only be capable of around twice that amount (32mm or more minimum object size to fill the frame -- with higher distortion).
The much better frame coverage of the 4500 would give you much more detail for your small stones (since they would be represented by more pixels in the image area occupied).
I guess we really need to know the purpose of the images (how they will be used). The 5400 may be a terrific choice for some purposes (and users are really found of it's 28mm wide angle, too).
If your photos are for onscreen viewing only, then most digital cameras will work fine (you can simply crop a portion of the image from the center, and a lower resolution image will work fine for onscreen viewing). I would make sure that I was getting a model that worked well at other than wide angle settings (like the Nikons), as well as one that gives you good control over depth of field (via Aperture Priority mode).
However, if you want to print a detailed photo of a tiny stone (at much larger than actual size), then this may require a totally different set of requirements from a camera.
Personally, if my primary use was for the best macros possible of tiny stones, and I planned on printing the images at larger than life sizes, I'd spring for the 4500 with the SL-1 Macro Cool-light.