I think that the big problem we're facing in both continuities is that in both cases circumstances were exceptional, so it's impossible to say if Shinji's reaction to Kaworu were a genuine attraction or a consequence of said circumstances and if said circumstances were different (as in meeting earlier in the story for example) Shinji would had reacted the same:
In NGE at the moment of their meeting, Shinji was at his lowest: Rei just died and was replaced by a clone, Asuka had a psychotic breakdown and disappeared, Misato completely invested herself in her quest to avenge Kaji, Touji is crippled and in a hospital bed partially due to Shinji's inaction (which makes him unable to face him or his classmates), and Gendo... well better not talk about him.
He's just so desperate for some emotional support and human warm, then out of nowhere comes this dashing young boy, Eva pilot like him, who isn't bonkers or crippled, and who completely and honestly opens to him, exactly what Shinji desperately craved for. But then, due to his ignorance of the Lilin ways and human interactions in general, Kaworu is very earnest in his interactions with Shinji, which confuse the young boy, who then profusely blushes at this dashing young man that's very earnest in his attitude. Does that means that Shinji just subconsciously came out of the closet, or is he merely confused by Kaworu's attitude, but take it in stride because he gives him the attention and emotional support he so desperately craves, and thus is confused about what all of that means about his sexuality?
Well it's kept ambiguous, and I think that it was Anno's intention so everyone could see what they want into that relationship.
Now in NTE the situation is different: first like in NGE, contrary to what you say obliterates, Shinji does show reactions to other girls even in situations where they are naked: first indeed he didn't reacted when Mari slammed her breast in his face, but it has more to do with the fact that he didn't had the time to process what was happening and that he got his head slammed against the ground, and that kill any boner, but he did blushed when Mari started to sniff him, also when Asuka installed herself in his futon, he did blushed. As for his reactions toward Kaji, well he got a man in his thirties that flirted with him and tried to kiss him, anyone would had reacted that way, even if it's later revealed to had been a joke.
But that's not the more important point, the second and more important thing here is that by the time of Q, there's already someone he's very close to, whom could be considered a love interest (if he wasn't so emotionally and socially crippled that he can't even identify what he feels and how act toward it) which is Rei, and even more importantly, for Shinji she was still around and alive!
Also, Shinji wasn't yet feeling totally miserable and alone (notably because he thought that Rei was still here with him), but extremely confused at the situation and how everyone acts, and seeks not emotional support and human warmth, but answers about WTF is happening.
And those different circumstances shows in how Shinji interact and react to Kaworu, and contrary to popular belief, I feels that the "Ho Yay" was largely toned down in NTE. Sure there are moments like the "gay piano" scene as it was "lovely" nicknamed or Kaworu's memetic pose when talking to Shinji when they were stargazing, but that's a long way from Shinji blushing furiously at the mere sight of Kaworu, both taking a freaking bath together or sleeping in the same room.
Since we're all about little symbolisms hidden in any scene, lets compare Shinji's reaction when they meet for the first time in NGE and NTE: in NGE, Shinji immediately blushes and very prominently, while in Q, Shinji merely looks at him and resume his walk with Rei Q, clearly thinking something along the lines of "hey, there's actually someone else alive here, and he's playing piano in the middle of EVA-01's cage, weird.", not a single blush in sight.
Avatar: THE HIGHEST OF ALL HIGHS WE AAAAAAAAAARE!!!Kensuke is a military otaku who, at one point, is shown creepily taking pictures of girls to sell. He would clearly fit right in as an animator at Studio Gainax. -- Compiling_AutumnEoTV is a therapist, EoE is a drill instructor. -- ChuckmanSeriously, that is the most fananked theory I've ever heard, more than Mari being Marty McFly travelling through time to keep her parents (Asushin) together. -- Jäeger