I think you're forgetting that this is still a children's game.
The Smogon faithful (or even the Serebii noobs) garner such a small part of the market that no game will ever be designed for us.
That, right there, is the crux of the issue, alas. But it would be possible for it to be overcome, and I can think of a good reason for NindFreak to do it.
I really wonder just what the demographic breakdown of Pokemon players is. Isn't it true that at this year's VGC, the turnout for the 13+ bracket was about twice that as for the <13?
It would be quite natural for the games to age with the audience (Nintendo could keep making Mystery Dungeon and Ranger for the younger folks) and, quite frankly, keep us playing and buying their games. If they started going after the 18-35 demographic, there's one big advantage: WE HAVE MONEY AND DON'T NEED TO ASK OUR PARENTS.
Turning to HOW this could get done, Gameplay is one issue, and I really think they should move to an Active Time Battle format at some point (look at FFIV--really not that difficult to pick up, especially if you use the "Wait" variant). Beyond that, I'd say the gameplay is as mature as you want it to be, what with the depth inherent in EVs, IVs and breeding.
The maturity of the story is another issue, and it's fluctuated over the years. DPP did have Pokemon torture, but consider Colosseum and XD (the former, especially): set in a post-apocalyptic wasteland (by my interpretation) where pokemon stealing actually happens (and is condoned!), and criminal gangs roam the earth. And all that to say nothing of the disturbed and violent Shadow Pokemon, who can only be "purified" through a long and tiring process of, essentially, Pokemon therapy.
Honestly, I think what's holding the games back is the anime. While the maturity of the anime does indeed fluctuate, with Various movies had Pokemon death (and not just implied, and not just the kind that tears bring back to life), the bottom line is that animation in the US (anime in particular) suffers from what TV Tropes calls "The Animation Ghetto," where anything with cartoons is assumed to be for kids (the flip side, of course, is "All Anime is Naughty Tentacles," which doesn't help the cause, either), so I think we're kinda screwed, there...
I realize I'm kinda rambling, and where I guess I'm landing on it is this: if the video games existed alone, I think NintendFreak would let the games age and mature, as they would probably be rewarded with MORE sales, not fewer. However, the anime is holding it back, and considering that Nintendo makes probably an equivalent amount on merchandising as they do on the main series video games, I think we're hosed, at least as long as Anime in the US is perceived as only for kids and sex perverts.