To be honest, I'm not sure I'm entirely happy with any of the Affinities, and wouldn't really want to see humanity's future go down any of their paths. Presumably because of the demands of gameplay and to play off of science fiction archetypes, they all have their flaws and limitations -- particularly in their demand for conformity to their particular philosophies from all members of their societies.
For me, an ideal form of transhumanism would be the sort portrayed in Iain M. Banks' Culture, or the Golden Oecumene in John C. Wright's The Golden Age -- societies where people could freely chose what bodies or shapes they wanted to adopt. Whether one wanted to be a transhuman ubermensch, become integrated into an alien species, or have one's mind uploaded digitally and use a starship for a body, all were permitted and acceptable (even if individuals still had aesthetic preferences -- one of the characters in The Golden Age dislikes having to interact with individuals who adopt brutally geometric cyborg bodies, for example).
I suppose, in the end, I don't really associate "humanity" with possessing a particular physical shape or composition, but instead being a product of one's thoughts, beliefs, and actions. As such, I guess I trend most towards Supremacy, as I have no particular issue with someone who may want to become a cyborg or digitally upload themselves to puppet around a robot body. But at the same time, I couldn't really see making any such change mandatory, as the Emancipation victory would seem to apply. An ideal society would be one in which people could choose whichever body type they wanted, whether baseline human, cyborg, or alien hybrid, of their own volition without any coercion.