Unfortunately, most examples I can think of aren't translated, but in case you or anyone else who's interested happen to read Japanese (or if they eventually do get translated), here are some I've come across:
Tomiko no Kimochi - An important side character is transgender and has a girlfriend. A surprisingly realistic and respectful depiction.
Otome Danshi ni Koi suru Otome - Female main character falls in love with a "pretty onee-san", who turns out to be biologically male. Though not outright stated, "he" (as he refers to himself) appears to be agender, but leaning female. Enjoyable, though with a fair share of jokes regarding the issue.
Uchi no Danna wa Oyome-san - Female MC is married to an untransitioned MTF "man", who switches between male and female mode, depending on the situation (e.g. male for work meetings etc.). Haven't finished it, but it seemed worth the read. Slight [Het] warning though, as people tend to swoon for the "male" mode.
Half and Half (Nanami Mao) - Translated - MC is in love with her childhood friend, who as an adult came out as transgender. A strange mix of realistic and idealistic/tropey, but worth the read. As has been mentioned in other threads, however, the transgender character is mainly referred to as "he", though I don't know if the author or translation is to blame.
Edit: (And if y'all don't mind pre-transition smut in text form, I might as well shill my own writing.)
last edited at Apr 4, 2018 10:38AM