Phase 3 is the removal of subclasses from a gameplay perspective, but instead subclass trainers offer “challenge quests” which, according to berezaa, may take multiple days if not longer to complete, and are ridiculously challenging. You can begin the quests at level 20, 30, 40 (maybe) and 50.
What’s the reward for these quests? The ability to learn one of the abilities from the subclasses. These are pretty expensive to learn, though.
Keep in mind, if you felt like it (although it would be really time consuming, expensive in terms of AP and difficult to pull off), you could do multiple subclass quests on the same slot, and end up with abilities from different subclasses.
Each “next level” quest requires you to complete the previous quest of the subclass (for example, you can’t do the level 30 Knight quest without having completed the level 20 Knight quest). Bear in mind, (I think) even if you’re over the required level for it, you can still go back and complete it. berezaa said that he expects most people to just stick with one subclass the first run-through of the game, because doing a bunch of them would be too tedious, but when they reach the end of the game people might go back and do the others one to unlock different skills to play around with.
The level 50 questlines are special though, being the hardest quests in the game. When you complete them, they gives you the subclass mastery set, which is the armour that the subclass trainer wears. The armour gives you the “ultimate” subclass ability when equipped (for example, Resurrect is tied to the Cleric robes, essentially making them a Cleric in general).
Combined with phase 2, by using the ultimate ability enough (although much more than normal perk unlocks), you can learn the ultimate ability for a large amount of AP without having to equip the armour set itself.
This means that you could theoretically unlock every ultimate ability in the game, and have them equipped together (though this means forfeiting pretty much every other ability or perk equippable), but this would take a ridiculous amount of work to do, and would only be for the most dedicated players to use.
Keep in mind, despite all of these major changes, you can’t jump major factions to unlock abilities. For example, you can’t unlock Assassin skills as a Warrior.