The two were not over-the-top or used as plot devices, but rather, their relationship was central to their characters and was very relatable. Their relationship was not explicit, but it generated a ton of hate among anime fandoms that were not happy with the gay overtones bleeding over into a not-so-shounen-ai sci-fi series.
The controversy these two caused upon No. 6's legacy shouldn't be how many homophobes it pissed off, but rather its captivating storytelling, surreal concepts, and endearing same-sex relationship. These two characters are incredibly interesting separately. One might have missed this crucial and brief scene that makes the nature of their relationship and subsequent sexual identities pretty clear.