Aline suggested switching normal movement and hover so you're normally a bit slower but can 'sprint' and I think I might change that in the directors cut because it seems sensible.
The flickering is light through the bees wings :D But yeay, i need to make those non shadow-casting I think because I noticed it a few places too, good eye !
The spray does 2 types of damage, there's an initial hit, then you take damage over time... its definitely a bit extreme in the build but i've worked on that (particularly fixed that if you are in multiple clouds you dont just insta die :D ) - that's some good playtesting
Theres various reasons for all of what you said, I don't think your wrong about anything, I think i've already fixed, planned to fix, or changed everything you've mentioned so good to know most of the things i've noticed are real ... director's cut should be solid.
Considering changing health to stamina and making you fall to the ground if you run out so you never 'die' but you have to sit around for a bit. This would be combined with putting in a timer so you have to reach the end of the level before nightfall (when bees can't fly around) which would be the 'game over' condition ... what do you think ?