NGE: A thematic addressing of, amongst other things, the schizoid lifestyle of obsessive anime fans, with Shinji as the principal avatar.
NTE (especially Q): A thematic addressing of, amongst other things, the dependent lifestyle born from EVA obsession, those "so inflated" fanatics who let the series' fictional characters and mythos become unhealthily important (becoming an unintended replacement for real interpersonal currency).
This has always seemed to me to be a readily apparent reading, if not necessarily of the preeminent theme but a secondary one. Shinji's place as a self-insert for both Anno and the Anno-like audience has always been established; that his prevailing totem (in Q assuredly) is a viewer base echoing his own disorientation, indignant claim to immediate clarification and desparate solicitations for emotional complimentation in lieu of an obvious channeling of Anno's own state of mind is inconsequential (or at least completely plausible, as there needn't be an adherence to the thematic dynamic of NGE/EoE Shinji).
'Death of the author' is bandied about often in EVA analysis. Its applicability is only as an supplement, reminding one to view a work both as an internally consistent narrative with its own thematic and tonal personality whose philosophical underpinnings can be derived from the text itself, and from the 'authorial intent' perspective wherein Anno's purposeful self-reflection, directed viewer dialogue, and sociological/psychological sentiments bear significant weight in their shaping of the narrative structure, character dynamics, and overall atmosphere. Neither is more important than the other, but both are immensely interesting and together create an appreciation greater than either taken alone.
In my estimation , EVA shines brightest when it calls out to the audience to force self-awareness, appreciated or not. That the entire franchise always plays with a notion of self-destruction (i.e. a brilliant anime imploring the viewer to advance beyond anime, beyond itself) gives it a cutting honesty and not-so-lightly employed hypocrisy to keep one thinking about its disparate themes for years on end.