I read the ending quite differently.

!Gendo's only goal in instrumentality was to reunite with his wife, and NERV/SEELE were just after power. Shinji actively rejected both of these goals by restoring the bodies of those who did not wish to be part of the hivemind. The ending was him realizing that the challenges of being human were mutually inclusive with the emotions of love and trust; the human body is effectively an AT field borne of the fear of being truly known by others, and love is the result of trusting others to view part of that "true self." Instrumentality would've made Shinji's life a lot easier, but he would've also lost the relationships he'd built with the people he'd actually come to care for. Also, instrumentality didn't end the angel threat, rather the angels all had to be killed before instrumentality was initiated to ensure they didn't just wipe out the human race.!<