1. Haven is just Town Square, Arcade, Bazaar, Garrison, Lab, Advanced Training Hall, and Hall of Heroes. It's not really supposed to be a mysterious place that you explore to discover secrets. It's supposed to be home.
2. Have you read the wiki page Achievements?
3. You might be confusing the Clockworks with the Core. The Core is seen in only one mission (Dreams and Nightmares), and kind-of-seen in Shadow Lairs. It's always pretty much the same. But the Clockworks is a pretty big and diverse place. Some parts of the Clockworks are highly random, and other parts are carefully planned.
Yes, end-game gameplay is great. The game gets much more challenging as you progress through it. You sometimes see complaints on the forums, usually of two kinds. (A) 5-star Radiant Fire Crystals are hard to get, so completing your 5-star equipment takes a long time. (B) Players burn through the content and then complain about the lack of new content. This is life.
4. You should work your way through the rank missions. There are a few in rank 2-2 and 4-1 or 4-2 that explain alchemy. Or you can just read the wiki page Crafting.
In general, our wiki isn't perfect, but there's a huge amount of information, so check it out. And welcome to the game. :)
