I've always been a proponent of keeping classes in as I appreciate the added flexibility of them (although the transition to 2.0 really nerfed the heck out of it from what I understand), but I also realize just how much of a... hindrance, I guess, that they are to progression in both a gameplay and lore sense. That being said, it really wouldn't be too hard to change the lore. That would, in my opinion, be by far the easiest thing to do if they removed classes. It's the change in the game system that would be exceptionally difficult to change. But looking at lore first...
Come 3.0, would it really be that hard to add in something along the lines of "After having granted certain adventurers Soul Crystals, we were able to find ways to return the lost arts of *insert job here* and they are now available to all to master." The 1-30 class quests can stay the same in storyline, and once completing the first level 30 quest you're told to go visit so-and-so as they're able to teach you a way to gain greater power, which is pretty much what happens anyway. Then, from 30-50 the job quests would change to be something else that fits more with the lore. Unfortunately, this would mean that the old quests could no longer be done, and people who are already at 50 couldn't see these new ones (unless, y'know, SE could have them make sense retroactively), but it's a give and take. The 50-60 quests would take this into account and maybe have the NPCs react to whether or not you reached 50 pre-Heavensward or post-Heavensward. Overall, it could be explained away easily how jobs are now available to all.
Then we have the change in the game system...oh boy. First off, to accommodate any changes in lore, the actual content of the quests from 30-50 would have to be changed, which means remaking around 50 quests from scratch. Second, changing the cross-class system into a cross-skill system would require a lot of recoding and rebalancing work that the dev-team may not have time for. It may actually be a bit more beneficial if that'd let them give us more options for bringing skills over to other classes, but when compared to the work it requires...I'd rather have new content, not remade content. Third, fixing gear so that it applies to jobs and not classes--more recoding of every single piece. Of course, we also have the ACN/SMN/SCH problem of how the heck that'd work, as some people don't want to lose their Carbuncles or Egis (I want to keep my Carbuncles, too, by the way), but also want to be able to separate their stats. Also, tying in with both lore and game systems, would they still require us to have a secondary job leveled to access the level 30+ quests? If not, I could see a bunch of WARs without Provoke because "lol I want to play WAR not PLD" or a bunch of SCHs without Stoneskin or even Protect. If so, players would be complaining about how other players aren't coming into dungeons or trials prepared because SE didn't require them to experience other classes and gain abilities from them.
Feel free to correct me if I'm making too big a deal of something, am missing something, or have misrepresented something--I'm certainly not a game developer or programmer in any capacity, but these just some things that came to mind reading through this topic. Sorry for the wall of text, but once I started I just couldn't stop, heh.