As for the story, that's just Game Freak getting stale with storylines. I'm quite tired of it myself, the same formula being repeated like it is, but Game Freak knows people will buy it no matter what so they keep doing it. I think really they need to try something else concerning the main story, like time travel or an exploration aspect or something. It doesn't really need to be a doomsday cult every single time; it could be something else. The only thing that made Team Flare really stand out was the fact they outright wanted genocide, which is both disturbing and dumb when you think about it.
Furstratingly Game Freak have also shown that they can tell good stories. BW despite flaws was certainly a step forward, and in gen six both the Looker sidequest and especially the Sea Mauville story were much more interesting and better written. It needed be more epic, it just needs to be better delivered.
I don't think we'll get much in the way of darker stories, leastways for the main games but probably nothing darker than anything we've already seen. Mind you, not all Pokemon games are cutsey (I haven't played them but I heard mentions of suicide themes in MD, and Pokemon Colosseum/XD had 'Shadow Pokemon' and heavily implies that these rogue and dangerous Pokemon have basically been tortured or somesuch into being so angry, even to the point of changing their appearance (Lugia).) But beyond this I don't think we'll get much more 'mature' titles, in part because Pokemon is aimed at E for Everyone in the majority of games, or as low a rating as possible. I don't see a game centred on 'teenagers and adults' as was put earlier, and it's also worth remembering that many teenagers and adults are quite fine with the way Pokemon games are set in terms of atmosphere, flavour, etc. If you want something like Dark Souls, it's unlikely you will find that in Pokemon. You can't please everyone.
I get reprimanded quite a lot for disliking the fairy type. In my opinion there should have been a light type first.
I'll go on a slight tangent.
There's more written about both fairy and why there's no light type here, but I'll paraphrase on the latter - there's no light type because there's already one. That is, the fighting type is the light type. While you have the mind over brawn relation with Psychic vs Fighting, you also have the mental prowess defeated by dirty fighting. Look at the Dark type moves - Bite, Beat Up, Sucker Punch... all dirty tactics. So what beats Dark? The pure, honest fighting style - i.e. the Fighting Type. In that sense, you can view Fighting type as the 'light' type capable of beating the dark type, and hence there's no need for another type to come in and be that role.
(Also, not all Fairies are cutsey. Mawile for instance has an interesting basis in a Japanese folk tale regarding a woman with two mouths.)