First, it was he was in love with Reiji then it was really in love with his mum because Reiji looked like her then it was he hated both of them, then it was he wanted to be Yuko, and now we're back to him being in love with Reiji. We went in a complete circle the only real thing being gained was a feeling of wasted time and needless mind-fuckery. Don't get me wrong, there isn't anything substantially wrong with him being gay but if it was always intended for us to settle on that fact then why did we have to waste so much time (on Gen's flashbacks, etc.) playing around with the idea that he was never truly in love with Reiji but Yuko just to then shoot that plot horse dead with the empty reveal that he really wanted to be her, to then immediately trash that to go back to the original point of just being in love with him.
Also, if you take everything we have on Gen into consideration, this man is the least affected by the town, 80% of his crap and issues come from his own shit.