Portal Scrolls, Tomes & Tokens
These are items that give you access to certain uberquest. These can be one-time use (scroll), multi-use (tome) or infinite (token). This adds more items to the market that could be highly valuable. Not only will this allow you to access a certain uberquest, but there can be scrolls to access the same area on different places.
For example: we could have an item called "Valthek's Portal Scroll" that when used, creates a portal directly to the end of Yshari Sanctum. Then, you could give Valthek a 10% chance to spawn such item when killed (or it could be a regular drop in the uberquest). Or you could take it one step further and give Valthek a 0.5% chance to spawn a "Valthek's Portal Token" which could be used infinitely.
Of course this is just an hypotetical case, I'm not saying this will necessarily happen. You could have some less-impressive ones like "Assur's Portal Token" that would still be really good as it would make duncraig farming much more efficient (because it could be used in town).
Cube recipes would simply be taking scroll portals to the next level. When performing recipes, you can create complex conditional formulas based on different aspects from your character. This ranges from setting a level requirement or a class requirement to limiting access to characters that completed their class charms, for example. There are tons of other ways to limit access.
But another cool thing in spawning portals from recipes is that you could have one reagent that can give access to different areas, depending on what you cube it with. For example: let's say we have an item called "Catalyst of Let Me Try Again Plz" that when cubed with any charm would take you to that specific boss fight instantly, consuming your charm but saving you the walk to there.
Again hypotetical scenario, I'm just throwing ideas out there.
Missiles and Skills
Finally, portals could be spawned from missiles, and thus, skills, and thus, procs. For example, there could be a monster with high health and fast run speed (similar to Treasure Goblins in d3), that when killed, summons a portal to a specific quest. Then you could make this monster spawn very rarely on some or all levels. Another example would be for example, giving monsters in unformed land a 0.001% (or whatever) chance to spawn a portal to Hidden Fortress (where you fight Zorun Tzin), and remove the direct entrance on the level. This would add a farming requirement to access specific boss areas, rather than just skipping the whole thing.
This could also allow for multi-stage uberquests, where you can only transition to the next stage after the boss was killed.