I wonder if the issue is feature creep (common with complex projects) or having to re-invent the previous engine if major parts stopped being usable due to license or obsolescence issues.
One of the major ways to cope with either situation is to just enforce a pared down version with enough hooks for major updates. Given the digital distribution system, that seems quite doable.
Balancing is another possible issue and (given the previous removal of a planned class) sounds like a present concern. The thing is, trying too hard to balance a game can actually be wasted effort. The previous pattern of patches and DLCs make balancing by accretion a viable strategy. The inclusion of user-generated adventures and rewards is inherently going to change whatever balancing calculations are made at launch.A lot of that initial balancing can be achieved in a closed alpha or beta that allows the most obvious things to be mitigated. Later DLCs offer the ability to mitigate some of the later variance.
The next biggest cause for delay that I can think of is writing all the little bits of lore and keeping them consistent. That is a real challenge and disclosing it would risk getting the fan base emotionally invested in features. That said, the seeming lack of continuity can be explained by ... magic. And storylines explaining why some seemingly significant feature of year one is not visible now.
"But I saved the school from pirates five times! Why aren't you trusting me to go to the marketplace on my own?"
"You say that, Prof. Ayentyre said that, but do you want special treatment and all the doubts that come with it or to allow even Phillipe to be allowed near the Magical Snakes vendor?"
Change of faculty and bad record-keeping is another way to explain a seeming lack of respect for the adventures in year one.