Flying is cool. Being unable to fly over a broken bridge that my 8 str mage can jump over, is not. For example, on the caravan map, right before reaching Coparann, there is a broken bridge with one square between the two sides. Anyone can jump over that square, but if your character is flying, that character cannot cross. There are also several areas that you can jump across but cannot fly over.
This is immersion breaking. While I understand that being able to fly over any terrain may make any jumping "puzzles" obsolete, the solution should be to redesign the puzzle rather than awkwardly limiting the fly spell. (And, honestly, shooting a pillar to make it fall or having to cast jump on your fighter for the umpteenth time is not a fun "puzzle," it's a nuisance.) The current Fly spell is confusing because it is not clear which tiles are accessible via the spell, and it's downright frustrating when you are prevented from accessing an area that you would otherwise be able to without the spell.
Spider Climb suffers the same problem. For example, in the ancient library, there is a chest in a room where the floor has given way. The chest can be accessed by shooting a pillar down and walking across. However, the walls in the room are wholly intact, but a character with Spider Climb cannot walk on those walls to reach the chest. Again, these artificial limitations are immersion breaking.
If such travel needs to be prevented, there should be a plausible reasons for the limitation. Maybe the room has an anti-magic field, maybe the walls are covered in sheer ice, maybe the walls are crumbling and the weight of one's body causes it to fall apart, maybe the room is covered in webs that makes flying impossible.
Love the idea, but the execution needs some polish.