Since you asked, I shall try to add to whats here already. I won't bother wading through Smashchu's posts though. I skimmed through a fair bit, but not enough to make a full fledged counter argument.
Expand on the story by a fair bit. They started making some steps towards this with Pokemon Diamond and Pearl and it seemed to work out really well. The better you flesh out the story, the more you will sell to the casual JRPG crowd. The story kind of stagnated after RGB. There is a nice, living, breathing world they could use to help add to the feel of the game that would draw in a lot of one fanbase, and not at the expense of the others. The concept that the story hurts the game is almost laughable. It is a RPG at the end of the day. RPG's need story.
Secondly stop making clone pokemon. Starly is Pidgey with a different name. We all know it, and no one really likes it that much. Just fiddle around with the older existing ones to make them better. Starters can ignore this if you really want to. Starting someone with 3 types that have fairly obvious strengths and weaknesses is a good move. And even then with DPPt they managed to differentiate a lot of the starters from their earlier ones with the subtypes.
The HM situation seems to be stabilizing finally, but it went to far as Kylie said. Having to gimp various pokemon one move is really rough. Make the moves strong enough to use and it will all work out. I could not care less that one of my pokemon is required to have Surf for example. He was probably going to get it anyways. The move is bad ass, and arguably the best water move in the game. Do the same for a few other HMs and you can make it work well.
Continue to tweak and tune all the abilities while adding in more. This keeps the hardcore constantly busy readjusting to the new rule sets. If you change everything too often you will alienate them of course. But a fine round of tuning every gen keeps things interesting. I don't think it needs to be turned on its head like it was this generation, but something to keep the research going.
Add more stuff after you beat the Elite 4. Visiting old regions would fit this perfectly. I don't know if you could visit all of them, but at least a few. With RSE it would be hard since they had it occur at the same time as RGB. DPPt would have been a perfect time to go back to the RSE areas though. Sadly it didn't seem to work that way. Fortunately there is HG/SS to help even things out. It is possible that they see it as the solution, but I would still like more content per game. The addition of the battle tower is genius. Now they just need to keep tweaking.
Keep adding new pokemon should go without saying, but apparently it has to be put out there with this crowd. Catching the same old ones over and over again will get old. I hate caves cause I am sick to death of seeing Zubat and Geodude. I know them. I know how they play. I might use them briefly to fill a hole in my early team, but I would rather experiment with the new guys. Sometimes even the clones of old ones can have some surprising move combinations. Old fans will come back in greater numbers the more new stuff you add.
Make breeding much less of a pain. A lot of the competitive players are not using the game itself to play as much. They get their great team for the tournaments only after fiddling around with it on an emu server. When the most hardcore player see it as too much of a pain in the ass, then you have a broken system. Kylie's suggestion has some merit. I dunno if I would go exactly with it, but it is something.
Make the online system much more robust. People keep saying they want a MMO, but Pokemon as it stands wouldn't translate all that well into the genre. All you could really add is 3D battles, and easy to find online battle. Most of the popular suggestion would be plagued by problems and not implement well on a game of that scale. Flesh out the online match making, and expand to a few more options and you could satisfy the desire for a MMO though.
Thats the short version of what I think would help Pokemon sales. The series is monstrous in size already, so it is hard to say any major changes to the core mechanics should be made. Given that the series is showing growth again after some nasty decline is a very good sign. You can't directly compare userbase/sales ratios for anything remotely useful so I am just going to ignore the nonsense on that front. I suppose you could sum up the majority of my post by saying "follow the same path DPPt did," but I think there are a few areas they didn't get it quite right on.
I do have a few things to say about the misconception of legendaries though. For the most part they are not actually all that much better than the normal ones. Yes you have a good bit that are broken, but those are still relatively low compared to the total number of pokemon. I do agree they seem to be adding them at an obscene rate, but the truly broken ones aren't all that bad.
@Kyliedog
EV mechanics more or less work that way already. The breeding part is new, but EVs get capped universally. You can only get 255 EVs for any stat (and only use 252) and you cannot earn more than 510 EVs on any given pokemon. I think eliminating IVs would take too much out of the individual feel of the pokemon, but increasing the heritability of IVs would do wonders.