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Mobi doesn't support at least some of the features you're describing. Dropcaps for instance are definitely not supported in Mobi. I think the same is true of font embedding, not sure about Superscript.
Mobi is based on html 3.2, which is quite old and outdated. As to specific features it supports, you should probably ask on the mobi subforum on Mobileread instead of Calibre. Once you know what's supported you should get good results as long as you keep your epub sources within those confines.
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