Well, thinking more about this, I guess the main story will more than likely involve a villainous team trying to get their hands on a Legendary Pokémon to change/take over the world, as usual. But... I just want the storyline with the villains to be more direct, you know? Let me explain:
At times, I miss Team Rocket. First and foremost, they weren't that obtuse. Their goal was achieved well before your story began. They were dealing with smuggling and kidnapping, blackmailing, burglary and probably money laundering, what do I know. And running a somewhat legit casino. They were the mafia. They practically owned Kanto by the time Red showed up. They didn't really want to change the world, steal all the Pokémon or something equally farfetched. They wanted to keep the status quo, and your quest was to bring them down. They didn't dress up in (overly) stupid costumes, and their leader was a carismatic guy in a tuxedo and with a realistic hair style/colour (looking at you, Colress). Regular bandits, not radical extremists or rebels. In later games, Cipher and Team Snagem were much the same. Cipher, much like Team Rocket, wanted a strong legendary Pokémon, but they only wanted it to increase their efficiency at evildoing. They used it for robberies, instead of challenging the world order. After all, a successful villainous team is dependant on a functioning society to leech off, and they don't want to raise more attention than necessary. Sure, their goal is world domination, but they want to achieve it using sneaky means. You would hardly notice it the day they eventually took over.
All games since R/S/E have featured more ambitious and crazy villains, though. A "plot creep" has taken place, now there's always the world that is on stake. Defeat the villains, or face doomsday. I can see the logic behind that, it makes you more of a hero, but still... it's just not as plausible. It feels a little too forced that you singlehandedly save the world. Bringing down a local crime cartel by uncovering their hideouts and chasing their grunts out of several towns, then thwarting their takeover of some landmark, that seems a little more realistic. Heck, in G/S, you stop a hostage situation at the Radio Tower, and fix a sabotage attempt of the Railway in Kanto. You don't change the world, but you stop baddies you can relate to, and directly help a lot of people. In later games, you're pushed before The Pokémon That Created The World As We Know It, and disband the evil team by befriending it. Whoopity-woo.
Well, To elaborate on this, consider the image of the evil teams through the generations. We're starting at the most recent, with Team Plasma. They appear out of nowhere, tell people to release their Pokémon, and wander off. Everybody wonders "Who are those people? What do they want?" Then later, you stop them without the general population understanding much of what was happening. Goal: Take over the world. First by disarming the population, then failing that, blackmailing everybody using Kyurem to destroy those who resisted.
Team Galactic were equally bad, pretending to be in the energy business while secretly researching legendary Pokémon so they could shape the world to their image. Most inhabitants of Sinnoh guessed that they were up to no good, but their actions never really affected anybody. You stopped them before they could interfere with people's daily life. Goal: To create a new universe with Cyrus as god.
Team Aqua and Team Magma were also scheming guys who stuck to the shadows, and used science to fuel their environmental terrorism before searching out Kyogre and Groudon and trying to use them instead. They broke into places and stole stuff, built elaborate secret bases and used fancy equipment in pursuit of their goal. Goal: Changing the environment globally to better suit their favourite types of Pokémon. They never really revealed themselves to the general population, preferring to work without much interference.
Then, Team Rocket. First of all, when you encounter them, you see that they rule stuff in Kanto. Most of the region, seemingly apart from the remote Pallet-Viridian-Pewter area, is the playing ground of Team Rocket. Everybody talk about them. Everybody is afraid of them. The police are helpless. They make headlines in papers daily. They run businesses all over the region. Multiple regions, even. People talk about them everywhere. People are openly confessing, outright bragging, that they are members of Team Rocket. They are powerful and they know it. As far as I can recall at the top of my head, Vermilion City is the only settlement in eastern Kanto without a permanent Rocket presence. They have society in a vicegrip, and it's up to you to stop them. Goal: Acquiring money. Making profit. Stealing Pokémon. Continue until world domination is achieved.
I guess my point for my overall speculation and hopes for this storyline is that in XY, I wish for a little scaled-down plot, with an added "oomph". Legendaries that are powerful and rare, but not almighty and one-of-a-kind, and certainly not in charge of vital functions of the universe. Just a really strong, rare and revered creature that according to local lore appears from time to time. B/W was great in that regard, imo, there were no world-shaping legendaries there, yet they ran into world-destroying-territory when Kyurem was used to blackmail the entire region in BW2. Maybe I'm not the creative type in this, but... it'd be nice.