I’ve recently converted a few OTF fonts using otdtotfm (LY1 encoding) and written a corresponding .fd file; then a few more imports to get the font selection done and the thing worked very well together with pdftex and microtype. Some protrusion is applied (though I don’t know if it’s ‘perfect’ – whatever that would mean) – in fact there are much, much less overfull boxes than without microtype.
So if one cannot rely on the very latest additions to lua- or xetex and a small subset of characters is all right (though one can of course create as many fonts as to cover the whole character range of the original OTF file) this seems to be a valid option.