As Unicode has strived to replace all the existing standards with some success, I would recommend using it. I have worked and maintained a font using Unicode for some time and am not aware of any issues that arise from this. With everything else, I would not be surprised if you run into compatibility issues.
There is a lot, which isn’t covered by ISO-8859-1 (and its successors).
The codes exist for the small capitals.
Where have you found these? There are no small caps (as in the typographical emphasis) encoded in Unicode (and they will never be); there are only some phonetic and Cyrillic characters which look like latin small caps (but they shouldn’t be used for small caps).
But where to place the alternate characters versions and the extra ligatures ? Are there some rules for that ?
The Unicode-conform way of doing so would be to use the Private-Use Areas (PUA), but this is only to provide an alternative access to these characters for people using programs that do not support OpenType and similar. In principle, you could leave these characters unencoded (
-1 in FontForge). The latter is (or was) the only way to ensure that a text with ligatures or similar was properly copyable in PDFs created by some programs (so, to cover everything, use an unencoded glyph for the ligature and have a clone of it in the PUA).