Chit-Chat: The Anime Chat Café

*The kiss scene is indeed meant to be Serena kissing Satoshi, and his reaction to it is surprised awe, any ambiguity the scene has is so they could get it on TV in the first place.
*Likewise, you're meant to hope and assume the two of them are going to become a couple later.
*The idea to have a romance subplot apparently came from producer Shukichi Kanda, who came up with the idea of portraying things through a female lead's admiration for Satoshi, which then led to the suggestion that they'd have a flashback to a childhood meeting with romantic implications.
*Yajima did not know exactly how long the series would last, only that it would have to end when the next games came out.
*Alan was always meant to be part of the main series. The reason the four Mega specials were made was because it would be difficult to set up his backstory and development in the series itself, so he came up with the idea of giving him his own episodes that could establish his character. The idea to give these episodes a mega evolution theme came later, and was also his idea (so they were not made for the purpose of marketing megas, or in order to test the water for a series with another main character or any other such theory).
*Also, Alan is meant to be an "Anakin Skywalker-type character", someone who turns to the dark side to protect those he loves.
*Satoshi's XY design was primarily Yajima's, and the idea for his sideburns were taken from "a character from the video games named Red, which Satoshi is based on".
*Yajima wanted to make the bond between Satoshi and Gekkouga (Greninja) a major part of the story, but felt it would be difficult to do so if it had to remain a Gekkouga, so he went to Game Freak, and they came up with the idea of a synchro transformation. It was put in Sun/Moon afterwards, but was created during this discussion between anime staff and GF.
*The interviewer notes that Okido (Oak) didn't appear at all outside of episode 3, and that Okido's lecture segment getting replaced with PokeTV when XY&Z started meant that Okido didn't appear at all throughout all of XY&Z (the interview was conducted before XY&Z47 had aired) and asks if there was a reason for this. Yajima confirms this was a complete oversight, not something intentional. Presumably this goes for other callbacks to older series as well.
*When XY&Z started, Yajima knew that the series had to wrap up everything in only a year, and they did a meeting to basically set up how the events of that year would go. He also specifically says that this is the reason there's minimal filler in XY&Z, there was absolutely no room.
*Yajima wanted to drop the use of stock footage completely, but this wasn't possible to do, so they went with creating stock foreground footage that could have different backgrounds added to it instead.