I wanted to form this discussion because of all the hatred and rage I've seen floating around the forums on what people think will happen to the canon in TES 6 so here's what I think is very possible. (Whilst exploring Skyrim I did have the chance to read up on plenty of the Lore and I'm going to make some assumptions based on this don't shoot me down. None of us really know for sure.)
1) It's been stated before but I believe that the Dragonborn will end up siding with Ulfric. (This is entirely based on the principle that I sure as hell wouldn't help the people that tried to cut my head off.) That and in reading the book the Bear of Markath it can be safely assumed that Ulfric is a skilled leader of troops, and a cruel warlord (It mentions in the book that he put everyone to the sword that didn't help him women, children, elderly the whole bunch.) This fact paired with the brutality of the Nords makes it seem much more likely that Ulfric and his Stormcloaks will just out do the legion with sheer force and religious zeal (Think about the U.S. position in the middle east, religious factions are always a wildcard)
2) The reforming of the Dawnguard will be canon (This is based on the fact that in the book called A timeline of the 3rd era, or something like that....It's in farengar's little area, it's stated that the reformation of The Knights of the Nine became Canon so I think we can safely assume that the Vampires didn't win this one and Molag Bal will have to look for another outlook on power.) This will help replace the very shortlived Vigilants of Stendar that we're completely steam-rolled by Harkon's Vampires. This opens up a new order for combating both Vampires and other Daedra creations.
3) With the death of Alduin and the Last of the Dragonborn being...well born, we'll effectively see the Blades on the way out as the protectors of the Dragonborn (Hopefully Bethesda won't botch this by making Dragons still Viable because I'd love for the Blades to have a bigger role in the next TES)
4) With most of Tamriel in the toilet and the Empire effectively defeated the next TES will have to focus on the coming of power of a New Government (Empire, Dominion, or a Third Party?) The Empire has nearly collapsed in Skyrim and with Stormcloak Victory the Empire will have croaked (Refer to 1)
5) An overhaul of the guild systems within the Empire (Skyrim avoided this by having the College and the Companions but if the next TES takes place in an area that has been colonized further by the Empire then we'll see The Mages guild and the Fighter's guild undergoing some exciting changes.
These are my main thoughts. Be sure to tear them to pieces (Nicely if you can) I love hearing other peoples opinions on this matter.
One final note though...Can someone please agree with me that the next TES should be complete Anarchy? I want to see a land in total Ruin. I want the player to have to be that Pheonix that rises from the Ashes....Hell lets see a Mortal born with the Soul of an Aedra or perhaps another character that can amount to Tiber Septim....but for godsakes Bethesda can we please have a game that doesn't just cater to the Mases? I want a game that pisses me off. I want everything that I wanted to happen to be taken from me. I want to find myself in a Tamriel that is Alien to me because outside forces have invaded (Ahem Akaviri please come and pillage my countries) I want to buy the next TES and be shocked at what's happened....Ok I'm done. =P