Thanks for the feedback! Yeah, I agree with pretty much everything you're saying. It's funny, originally when I was brainstorming and decided on this idea I just assumed I'd have the player control a lot of the game using the mouse. It wasn't until I sat down and started coding that I realized I couldn't do that, so the existing tool wheel seemed like the simplest way to do what I was trying to do while only using the arrow keys. It's definitely clunky though.
In retrospect I could have probably simplified the different tools into contextual actions (Like press and hold to till a tile/dig up a plant, do a short press to water plants, etc) so that you only would need to use the tool wheel to select the seeds. Giving the player a lump sum of money at the end of each wave probably would have helped with your other point.