Stramyst and dandan, you're both correct! Shinji's definitely wearing the same swimsuit as Rei and Asuka. This is from the Shinji Ikari Raising Project.
For one week of the game, the pilots all engage in a special synchronization training - and what better way to training that than synchronized swimming, eh? I don't speak Japanese so I don't know exactly what happens in the event to provoke this scene (and it's been a while since I last played, as well)... but I'm sure it probably involves accusations of perversion.
