First of all, thank you for the feedback.
The fact that you can collect drops simply by hovering over them—rather than having to click on them—is the result of improvements made in recent updates. The text stating that you need to click to collect them is a leftover from the game's early versions.
Most of the other questions you asked should be covered in the settings menu, specifically under the "Game Mechanics" and "How to Play" sections.
I understand that the game is difficult; that was actually my intention. Imagine a game where you have to collect drops, manage the Bio-Weapon's targeting, set up and upgrade turrets, and upgrade the Bio-Weapon itself—all while fighting off incoming hordes and dealing with debuffs inflicted by the bosses you defeat. And finally, dying. That’s actually where the game restarts: beginning a new run with the skills you earned in the previous one.
My goal certainly isn't to create an "unintuitive game," and I agree with you on that point. While in-game tutorials do appear at the top of the screen, it is very difficult for a player to read them while juggling so many other tasks. However, I don't want to disrupt the game's pacing by adding a tutorial that stops the action and points a giant arrow at something saying "click here."