Well of all people it was Maya he had the hardest time forgetting at the end of IS (evidently). So it's not that farfetched. I already felt in that game Maya x Tatsuya was the 'canon' ship although Jun was my fav character and i liked that pairing better. I guess it doesn't matter since none of those ships mattered in the end.

Tatsuya had feelings for Maya, I'm not questioning that. But IS makes it clear multiple times Maya only sees Tatsuya as a "little brother" and the most she ever goes is teasing him for "liking older women". The feelings Maya has in EP are her subconsciously remembering him as a "younger brother" but Tadashi decided to twist that into romantic feelings. Maya as a character outside of this also always expresses a lack of interest in romance, which I believe was meant to mirror Artemis' mythology. (there are a lot of parallels like that between the characters and their personas in P2)