The link is the continuity. We have development for characters play out over multiple expansions. Our relationship to those characters directly ties into that. Iceheart would be just some random rebel leader without her introduction in 2.4. One of the most emotional scenes in HW story would have substantially less impact if we didn't already have establish relationships with characters involved. This is true for enemies and allies.
Now you could argue that they could just have it so you step into the existing story at that point and it would be like reading a series of novels and starting half way through. That's basically what the Story Jump potion does. The reason they cant just do this without something like a Jump Potion seems to be that their questing/gating system isn't designed for it and while it would be better for that to be fixed, it would also be a massive amount of work to overhaul a core system and that is something that is less realistic to expect.
The reality is the game engine we have is what they have to work with. Any solutions have to work within those confines. As you point out SE is a business and any major investments of money need to be justified to investors. They need to feel the returns are worth the cost. MMOs are these days already rather unpopular with investors simply because of the high risk and the rather smaller ratio of profit to investment compared to other game. Case in point look at Blizzard. Hearthstone has a vastly higher profit to cost ratio compared to WoW and required a tiny team to create.
There is going to be a cap on the realistic amount of resources a dev team can ask for and that has to be divided up among all the game's projects. This time round its Server infrastructure (for a inventory size increase), the patch development and the expansion. If we were to get a quest system overhaul it would come at the cost of one of those things.
You can complain about design mistakes in the past till the cows come home and it won't change the fact that the system we have is the one they have to work with. If we want to keep playing this game its that system they have to get to work.