This is a very good question, and I heard a lot of rumours, suggestions, and doom-saying about what will or will not occur. What we DO know for sure will change is:

1) Maps
2) (Inferred from #1) Mob Locations
3) (Inferred from #1) Details on quest locations/routes
4) New GUI
5) (Inferred from #4) Adjustments to battle mechanics (scope, unknown).

Some things that are not clear (to me at least, as I do not see a specific dev post saying otherwise) are:

1) Will the Primal fights still be around to fight? (And will they be adjusted)
2) Will the Primals still drop the same items?
3) Will Toto-Rak/DH/DH2/CC still exist, and will they contain the same items?
4) Will existing Grand Company quests be removed or change?
5) What existing classes/jobs/etc be merged, changed, or significantly altered?
6) Will there be more Hildibrand quests?


These questions, and many more, will be answered in next year's release of 2.0.


Thank you.