One-time use of scrolls, including in battle (even just from the active slots), can still be a huge imbalance. On the one hand, it can greatly increase the ways to conquer a specific map, and on the other hand, it can practically eliminate many interesting and challenging battles, especially in the early game. Unless there are usually few wells generated on the map. We could leave this possibility only for control scrolls (and not come up with a way to implement it in battle). Or make it a bit more exotic, allowing "burning" scrolls in battle if there is no (upd. not built) corresponding guild level. Such a "barbaric" approach.
Regarding "useless" skills and artifacts, I'm in favor of leaving everything as it is. Some things can be tried to be improved. For example, increase Mysticism, Learning - allowing the recording of scrolls of levels 1-3, 4, and 5 in the book.
Improving individual units is also an interesting topic. You can adjust stats, or you can add unique properties. The latter seems more interesting to me. Personally, I like the idea of a "ghostly" creature from Warlords of the Ancient World, but I don't know who to give it to so that it would be "lore-friendly." Demons are already strong. For example, giving Pit Lords two demonizations (under their own hero / for the entire battle (to everyone) / only to humans) could also be interesting.
Regarding new spells, a "scouting" spell seems appropriate for the magic of air. It could be made a unique spell when developing the Scouting skill, with fixed parameters at three levels.
Adding two more slots for primary skills seems quite reasonable with these new features