I think this feeling arises from social norms feeling unnatural to you. This feeling should be expected if your interests are relevant to this site, since people are not trying to be rational by default.

The difference between a pathetic misfit and and an admirable eccentric is their level of awesomeness. If you become good enough at anything relevant to other people, you don't have to live through their social expectations. Conform to the norms or rise above them.

Note that I think most social norms are nice to have, but this doesn't mean there aren't enough of the kind that make me feel alienated. It could be that the feeling of alienation is a necessary side effect of some beneficial cognitive change, in which case I'd try to cherish the feeling. I've found that rising to a leadership position diminishes the feeling significantly, however.