written in the stars
In my opinion, they should did everything they wanted (including Atlantica) in one game (Birth By Sleep).
You don't even know how long BBSv2 has been planned and you are already saying it should have been done in one game. For all we know, BBSv2 has been in Nomura's head since the start of BBS development. We already know he wanted to make a game based in the RoD since the beginning, this is the perfect opportunity for that.
And on Aqua, now while you say she is overrated, I think she is probably underrated by her many fans. They praise her fighting skills and ability to care for both of her friends (which Kairi only does half of the time, and only for the sake of Sora and not so much for Riku. Kairi-Riku interaction is based on her sleeping and him carrying her around and both vying for Sora's attention. Aqua cares equally for both of her friends...I'd have to say she is more of the Sora in the TAV trio...but that is neither here nor there) but they never pay attention to her failings. She is biased towards the Light, and her opinion is easily swayed by the words of other people.
I think that is why I like her more than Kairi and Xion (while Xion is third on my list, Namine and Aqua share first and second place, and Kairi is at the very bottom with the songs from Atlantica, Ice Cream Beat, and Vexen's creepy eye.) She isn't made to look perfect, but she definitely tries her hardest for her friends.
And on the points you made in your OP:
1) Kairi does not know how to fight. You'd think she'd know because she is best friends with two fighters, but there is no evidence she knows how to fight. Her swinging a Keyblade (and missing) at Heartless no more shows she knows how to fight than the brief time we saw her on DI in KH1. And in comparison to Xion and Aqua, she would have to be the weakest fighter in the series.
2) I like Xion, but I can definitely argue that she barely knew how to fight or use her Keyblade properly until after spending time with Roxas and slowly collecting Sora's memories. And I can also argue that her character is a deus ex machina when she 1-hit KO'd Xigbar. But again, that is neither here nor there. My point is that she also had to grow to gain her power, while we already knew Aqua was trained by time the events of BBS start.
3) We have no idea that Aqua is going to be the main character. We most likely will be playing this game with scenarios like the first BBS and with the secret ending, it would appear to be Mickey and Riku and possibly Kairi though unlikely.
4) Not many care about a game with Kairi as the main character. She is such an underdeveloped character that it would be better to develop her in the story before branching out and giving her a game, or her own scenario.
5) This is definitely not hyping up Aqua. If anything, this is milking the entire series as a whole.