I think a big part of the problem here is the auto levelling spells. I started a new game with 1.2 and early on things worked as they were supposed to: I did a mix of missions for spells and exploration for ingredients, found a few secret missions which gave me useful scrolls including a wind shelter or two, got enough stuff to take on a lieutenant, etc.
However, at around level 3, once I stockpiled some orbs and crafting ingredients (plus more from playing around with NPC dispatches) that changed; most of my spells were auto leveling at least once or twice, so even after killing the next lieutenant, I was immediately ready to move on to the next. No need to hunt for loot, so no finding much in the way of secret missions for buildings. The only obstacle that remained to progressing was wind shelters. In my experience so far in the game, it's really fun when I have multiple simultaneous goals and breaks down really badly when there's only one thing I want.
IMO an easy first part answer is to just lower the auto leveling amount by 1, i.e. Common - 0, Uncommon - 0, Rare - 1, Epic - 2, etc. Uncommon orbs aren't that rare, they're still desirable for the extra bonus modifier, and it seems self-defeating for the most common way to acquire materials for spells to directly cause you to need/want to do less of it.
I also feel like there should be some defensive upgrade that you want to make between lieutenant fights to go with the offensive upgrades. Perhaps shielding shouldn't be automatic but acquired somehow? Would that be too complex/unintuitive/hard to keep track of?
Re: the mission discussion, I think the way it's set up now is really good for the early game - gives new players some clear focus and direction and is OK for a while beyond that because it can tempt players with new modifiers or combinations they haven't seen (which is a note against all missions being hidden reward, although some could be). However, after a while, I just start doing a quick pass to make sure nothing I hadn't seen before popped up and then ignoring them. It seems like it's probably not necessary for 100% of world map missions to be spells. Maybe seed a few of the more essential scrolls at reduced rates as well?