@make_me_mad: The criticism is not that Atlus "chickened out", but that the outcome of the struggles is glossed over in the rest of the game or played for laughs. Yosuke's comment on the night of the camping trip is downright stupid (understandable in a way, but still stupid), Naoto turns into her polar opposite in the optional Christmas event. While Atlus is brave to attempt to discuss such topics in a game (a JRPG even), for some the way it handles the aftermath leaves a lot to be desired for. Like @chrissedoff mentioned, the way Atlus handled it could be seen as reinforcing the norm.
And Yosuke's ignorant behavior isn't glorified throughout the game. There are stupid jokes (because THEY'RE TEENAGERS) but by and large everyone accepts Kanji regardless of whether or not he's into dudes. The ultimate message is that it doesn't really matter either way, friends should always try to be there for each other and you should just go be happy no matter what you are. The identity politics is secondary. Naoto wears a schoolgirl outfit if you're in a relationship with her on Christmas because that's the sort of thing romantic partners do for each other behind closed doors sometimes. It wasn't trying to send some kind of message unless you're reading way too much into it.
The criticism seems to come primarily from people who really wished Atlus would've taken the opportunity to rub the players faces into hot-button issues to make themselves feel better. Ultimately, Atlus chose not to do that and took the more inclusive "what does it matter who we are or what people think we are? It doesn't change how you should treat someone else" approach, and now activist types just seem bitter for it.
Exactly. I think a lot of people are forgetting what it was like to be a teenager... how even now teenagers would use "gay" as a prejorative for something as simple as wearing a scarf. When it comes to Yosuke, he acts how lots of teenagers act when it comes to homosexuality but if asked honestly do they think LGB should have the same rights as everyone else, they'd likely say yes.