^takes some very tendentious effort to not count Kiana and Mei as one, and then you have the Orphanage pair... Seele finally got back into the corporeal world in the game's storyline a few chapters back (and became playable); many feels were had
Also everyone is kinda gay for Durandal-shamaa~ :v
Backstory-wise there's also Kallen and Yae Sakura who are quite canon but have the 'slight' problem of, well, having been dead for about five centuries and counting. The former being presently very much a (studiously preserved) corpse is the driving motivation of one of the story's primary not-quite-villains; while the latter is technically canonically a sort of ghost but has exactly zero presence in the main storyline, only appearing in a side chapter or two (and decidedly noncanon transient events).