I would also suggest that unless you have a very specific reason you should not embed the font. This will allow your readers to change the font using the capability of their ereaders.
Some specific reasons to embed:
- You need specific characters only available in that font.
- Stylistic reasons - Titles, quotes, etc.
Times New Roman is such a generic font that it should probably never be embedded. An exception would be if you're using some of the specific unicode ranges in it that are not available in others (eg. arabic or hebrew). TNR is a pretty comprehensive unicode font.
Troy