Another thing I think that tends to confuse people is just the ending period. The majority of mecha anime, and thereby the attitude with which mecha fans go into watching a mecha anime, are much more straight forward in action. Barring Gundam, most mecha shows (though I'm not a mecha fan, so correct me if I'm wrong) don't delve too deeply into extreme drama. And even Gundam's dramas tend towards the melodramas, not a real and explicit look into humanity, the driving force behind it, a person's existential crisis, etc. When you watch through basically all of Evangelion, while it may imply that the ending will be a look into the mind, it's a subtle implication. People get confused when suddenly there is no definitive, action-based ending and it all seems to be either a delusion or an alternate reality or... something, and they're not sure what. It really is the last couple of episodes that throw people since it's not what they're expecting at all.