At least Nintendo has apologized about not including same-sex relationships in Tomodachi Life and they intend to have a game with them in the future.
I wouldn't see it as lazy development really, there's minor mistakes in all games. Not sure what dialogue options are glitchy though? I've had my game since December and never got a glitch thing? But yeah, I mean, sometimes I call my friends "they" or "them" even if I've referred to them with gendered pronouns earlier or whatever. Maybe I'm just lazy too.
I use "they/them" all the time when talking about people as well. It never really occured to me that doing so was lazy or implied a different gender identity, since it's just neutral.
I dunno, I think I heard somewhere that the Japanese versions of Animal Crossing (as well as a lot of other media in Japan) avoid using "he/she". I've also heard that Nintendo of America only translates the games (the games are developed/coded in Japan, in Japanese).
If both of those bits of information are correct, then the translators were probably forced to use gender-neutral pronouns, because since they're only translating the game, they can't, say, add a conditional to check if the villager being referred to is male or female.
This is based on a lot of assumptions, so I could be flat out wrong on all accounts. I've taken quite a few Japanese classes, though, and I usually used "that person" instead of "he/she". And my computer science buddies and I dream of programming for Nintendo, but none of us are fluent in Japanese lol.