Here's some of the theories that I've formed, that's completely based on basically nothing, and doesn't even deserve the name of theory, but rather wishes. However, what Oda would do's probably better than my wishes so…
1. There'll be many more flash backs to the day that Roger was executed, and we'll get to know that much much much more happend that day, and that what happend that day will play a very huge role near the end of One Piece. Since so many seems to have been present at the execution: Smoker, Shanks, Buggy, probably also Sengoku, Aokiji, Akuinu and Garp. Oh, and Gol D. Roger too of course, much more might have happend that day than we know of now, much more then simply that the Pirate King was executed.
2. Blackbeard will beat Ace easily with his darkness logia-fruit, and then leave a by Blackbeard presumed dead Ace on Banaro. Ace is, although almost dead, still only unconscious. A couple of days later a merchant ship arrives at Banaro. They find Ace, still mortally wounded, first not knowing his identity, but when they find out that he's the world famous "Fire Fist" Ace, they see their chance of fame and money, and takes him with them. They pick the still unconscious Ace up and leave the island.
Several days later, Ace regains consciousness, and cannot remember what happend that day. After a longer time, he remembers the fight, and that Blackbeard preclaimed that he was after Luffy next. With this thought in his head Ace steals a lifeboat from the merchant-ship, in order to find Luffy and warn him before Blackbeard find Luffy.
Just after the end of the Fishman Island-arc, the Blackbeard Pirates arrive at Water 7. After a couple of hours, the Blackbeard pirates learn of that Luffy left the island several weeks ago. Angry, Blackbeard realises that he'll have to deal with Luffy later, because at the time present, his magnificent plan must be fulfilled. He gives his men order to head for a certain island in the New World, which he happends to have an Eternal Post to, since going there next is part of his plan.
3. After realising the over-confidence that Don Krieg placed in himself and his Pirate Fleet, Gin is disillusioned of the Don Krieg Pirate Armada, and leaves Krieg's crew in order to fulfill his own goals in the Grand Line. At the time being, Gin is somewhere in Grand Line.
4. Although appearing to be just another comic relief now, it'll later show that Buggy is more than the Jar Jar Binks that he appears to be. Close to the end of the One Piece, Buggy will unite with Luffy, since Buggy after all, is a pirate honouring the Pirate Ideal of nakamas, etc.
5. Just before or after the Strawhats have entered the New World, the marine realises that the only way to delete them before it's to late is to summon another Buster Call at them. By this time, the Strawhat's will be at a island with a big city, and the Marine is planning to destroy the entire island in order to get the Strawhats. Smoker will be involved in the Buster Call. When he realises what the Marine is willing to do, kill millions of civilians in order to get away with it, he begins to become more and more disillusioned with the Marine, the World Government and "Absolute Justice", but keeps to the marine. By the time, he's beginning to learn more and more about why the World Government is so upset with the Strawhats, and wonder what this whole Rio Poneglyf thing is all about. But just before the Buster Call is to go off, he realises that the good guys in this whole mess is actually the Strawhats, and just before the Buster Call will reach the island, he alone runs away from the marine in order to save the Strawhats. He informs them of the Buster Call that'll soon reach the island, and tells them to leave as fast as they can. He then gives them the best of luck and tell them that he hope that they'll reach the end of the Grand Line, Raftel, in order to once and for all put an end to the blood bath of the World Government.
Much later, on the run, the World Government has sent several marines to catch him, since he's charged for Treachery against the World Government, and defense of pirates. Just when he's about to die, Dragon shows up and saves him, killing the marines. Dragon invites Smoker to join the Revolutionaries, an invitation that Smoker accept.
Tashigi remains in the Marine, but is wondering more and more about Smoker's choice in leaving the Marine.
6. A great storm will force Shanks and Whitebeard to quit their fight, and the storm leads to their different ships drifting away from each other.
7. Somewhere in the New World, the Straw Hat's will end up at an enormous technological steam punk-island, where much of the One Piece-world's technology is developed. There they'll meet the famous dr. Vegapunk, an old scientist that appaers to be a crossover of Q from James Bond and professor Calculus of Tintin. Vegapunk isn't really a villain, but merely a scientist who lives for the pure pleasure of inventing and making scientific discoveries. However, the World Government is more or less forcing him to work for them, yet Vegapunk seems to have more or less no idea what his inventions are used for, as he seems to think that they'll go for a good cause. During this arc, dr. Vegapunk will befriend the Straw Hats.
It'll be on this island that Ener will return, together with the Space Pirates, and they'll attack the island. This will be where Ener is ultimatly defeated, and the same goes for the space pirates. The last alien technology will sadly enough be destroyd, preventing dr. Vegapunk from studing it, or alternative, Vegapunk will be killed during the arc.
This'll be the only times that aliens will interfere in the main story, and after this, will not be noted, as the people of One Piece has no idea of the existence of space pirates or whatever they are.
8. Raftel will be a good old fashioned priate island, like the ones in the Treasure Island, and will not be anything like "the planet D" or something that weird. Raftel will also feature ancient ruins, and will be in the center of a major misty cloud, sort of like Laputa in Castle in the Sky.
9. "D" could be derrived from Davy in Davy Jones, who already seems to be a real historical character in the Odaverse. It'll also be explained that Davy Jones was a great pirate who travelled the seas a couple of years after the fall of the Ancient Kingdom. Davy was one of the earliest recorded descendants of the ancient dynasty that once ruled the Ancient Kingdom.
9. The Ancient Kingdom was created over night, explaining why history before the Void Century wasn't also deleted.
10. The story will show more and more parallel with the myths of Atlantis.
11. The reason why it's so hard to get to Raftel is because of what it present at the island before you reach Raftel. A huge monster/natural phenomena/whatever-you-can-think-up-that-would-happend-to-be-a-bit-LOST-ish has caused that noone has been able to survive on that island long enough for the Log Post to charge.
12. At that island (which we actually have proof that it does exist, however, not that any of my theories about it would be true), which I will call Island Q (because Q is the letter before R as in Raftel), until Oda publish it's official name was where Whitebeard and Roger met for the last time. It was here that they finally came to agree and Whitebeard understood Roger, and why it was of uttermost importance that Roger reached Raftel. As of this, Whitebeard and his crew agreed to fight the gigantic monster at the island, giving Roger a chance to escape the island and get to Raftel. However, Whitebeard didn't manage to defeat whatever monster that was present at the island, and had to flee once Roger had managed to escape. Whitebeard was therefore mortally wounded for the rest of his life by it, which is why he still needs medical attention all the time.
13. Elbaf doesn't interfere with world politics, and the World Government has left Elbaf more or less independant, as they fear to try to make any agrements with the barbarians of Elbaf.
14. Tsuru and Garp have a long relationship, either as friends, rivals, or something like that. Tsuru might even be Luffy's paternal grandmother.
15. The Gurosei are like Spandam, no great warriors or anything like that, but merely tyrannic dictatorial politicians that rule the One Piece-world. This because One Piece is a manga, not a video-game where it's simply about beating the next and stronger boss. The Gurosei, I believe, depend on their Army, the Marine, the Cipher Pols and the Shichi Bukai in order to remain in power, sort of like the alliance system of Otto von Bismarck. They are in power because they're brilliant politicians, tacticians, and generals who knows how to avoid political conflict, not because they're some super-fighters strong enough to kick all their opponents's butts in face-to-face-combat. They aren't like Freiza or Piccolo in Dragon Ball.
That's about it.
I'll not even try to defend these theories, as I've earlier said, these are more hopes and wishes rather than theories, and I do not have the information needed in order to form any arguments in order to defend them.