Depends: Can I control my preference? Will it have an impact on the story? How "close" will we get?
To put it into perspective, in FF8, when Squall and Riona finally cuddle on the ship while traveling back home. It was a touching moment, but felt kinda shallow for me since I (as the player) liked Qustis better. Riona, for all her faults and trials, never felt like something solid but rather just a plot device. On the other hand, Qustis felt "real", as she leaves SeeD on her own volition to be with Squall. (Who I completely lose respect for in the first CD with his dooshbag attitude towards her.)
Compared to Cecil and Rosa of FF4, where they get separated for a large portion of the game, and finally reunite together halfway in after a narrow escape from danger. I felt those two should never leave each other ever again.
So to sum it up. If you're going to have a gay "main" character with a romance sub-plot, then make sure their romantic partner and the main character are simple enough to empathize with, and complex enough to have an rich untold backstory. If anyone remember in Earthbound, Jeff's friend and roommate that takes good care of him? He's quite awkward, shy, and questionable if he wanted to be "more then just friends", but He's also a powerful figure by the end of the game too. And not like "Super Awesome HYPER" power, but subtle and instrumental towards the defeat of Gigas.