Hi Some Pixel Guy,
It's an interesting idea you're working on here. I actually was thinking of doing something similar in the future, but it's not for anytime soon! Everything Chao Garden-like always attracts my attention :) I've played for about 45 minutes, maybe an hour. Here's my bit of feedback:
There's a bug with the UI when the Shop menu is opened without closing the Mission menu, and vice versa. The Open/Close button text is not correctly updated. It makes navigating the UI confusing. Also about the UI, I often would click a monster's name to upgrade it and realise I forgot to close whatever menu I had open. It a small thing but it gets irritating. I think menu navigation in general is a bit annoying, since the Open/Close buttons and the menus themselves are at opposite sides of the screen.
I found it weird that monsters are controlled with WASD, but the garden camera is controlled with the Arrow Keys. It seems to me it would be better if it was the same in both places.
Sound is really broken for me. It sounds very glitchy and gets too loud when I get many items at the same time.
I think you should be careful with making projectiles fade out slowly. It's hard to tell when they're fully gone and at what opacity they stop being dangerous. The gas spouting plants are confusing because of that.
I'm wondering about what kind of length you're aiming for with the game. I have no doubt you plan to add more levels, but I'm not sure how many times I can play the same levels over and over with little variance between each run. I think replayability is probably your biggest challenge with this project and I'm courius about how you'll tackle it.
I'll end on some positives :) I like the verticality of the levels. It's something I struggle with in my games; I find I naturally make flat levels. The movement is solid. The game is easy to get into; I understood the menus and controls pretty quick. Its an interesting idea like I said, so I hope you manage to finish the game!