In short, no one knows for certain. The implied Phoenix/Maya trend loses a bit of momentum in T&T and a new--or perhaps I should say old--contender (re)surfaces. Over the course of the game, Maya refers to herself as a "big sister" to Phoenix and during Case 2, they talk about how Pearl has "the wrong idea" about them. Phoenix says that outright. Maya proceeds to expound on Pearl's past and mindset, leaving it uncertain whether or not she shares Phoenix's stated opinion.
It is in the final case where the other contender (re)surfaces. When he meets her early on, they both find themselves staring mutely at each other for rather long stretches, though reasons other than love could easily be fueling these reactions. Maya immediately starts teasing Phoenix about her. During the night, they meet again and before they go to their respective beds, she gives him her hood as a good luck charm. Meanwhile, Maya has gone to a training facility on the other side of a bridge from where Phoenix is. That bridge is struck by lightning. Soon after, Phoenix sees this, attempts to run across the burning bridge in an effort to rescue Maya, and ends up falling into the river below. At this point, a murder has also occurred and the other woman is the defendant. At the end of the trial, the defendant confesses something to Phoenix which sheds a whole new light on their relationship and professes hope that he can one day forgive her. In essence, he does that. As the defendant--while innocent of murder--turns out to be guilty of tampering with evidence, she ends up in prison. During the ending, we see her at the Detention Center expressing thanks to Phoenix for visiting her and adding that while she was happy that his eyes were fixed on her for the duration of the visit, she felt a little bad watching Pearl give him a nosebleed.
For fear of taking a lot of the thrill out of the game for you, I will not tell you this woman's name, but I will say that she is pictured in my sig. When I finished T&T, well...my sig says it all, really.

We'll have to see if T&T affects
your pairing preferences.
