If you haven’t picked up a copy of Pokemon: Alpha Sapphire (or Omega Ruby) yet, you may not know about some of the comments that Team Aqua tends to make about members of the same sex. While in the original Sapphire, there were some various remarks as well (such as Shelly calling the player [regardless of gender] cute, before subsequently calling them disgusting), it was no where near the level it is at now.
Pokemon has never fully been known to queer bait, however they have recently been making more and more strides to include homosexual characters without downright saying that they are queer. Each game has had more and more elements added to it that would hint at characters having a non-heterosexual sexuality, and these characters have been increasing in importance as well.
Team Aqua (in Alpha Sapphire) is the newest adaptation to this trend of sexually ambiguous characters. Specifically the two admins.
Shelly, Team Aqua Admin
This is Shelly. In both the original Sapphire and Alpha Sapphire, she references the “cute” appearance of the protagonist. However, being a less ruthless version of herself in the remakes, she also says to the player “maybe we are destined to be together”. All of this completely disregards gender, giving the potential idea that Shelly is bisexual and finds the player “Cute” (but still considers them to be an enemy).
Matt, Team Aqua Admin
This is Matt. To be honest, I’m typically one that’s leans more towards Team Magma (because i loved Tabitha in the original games), but Matt is the big reason why I keep coming back to Team Aqua. Anyways, Matt is kind of the dumb oaf of the Aqua Admins (while Shelly is more of the brains, and the more ruthless one). Matt doesn’t make a lot of remarks towards the player in the original Sapphire, however in the remakes he’s noted in saying "I love interesting, strong dudes! That's why I love my bro, Archie! And that's why I'm gonna start loving you from now on, too! Next time I see you, I'll smash you up real good, OK?". He also later goes on to talk more about how much he loves Archie. While Archie never specifically shows a reciprocation of these feelings, Matt’s love for his “bro” Archie is often highlighted and leads to dialogue that could be considered slightly homoerotic.
While neither Shelly nor Matt have had definitive confirmations on their sexual orientations, it’s definitely something to think about when realizing how far the Pokemon company is coming along.