1- I love the graphics. They have a lot of character and you picked some nice colors for stuff. The pixel work is amazing throughout.
2- Music and sound effects were also good, though there are still some things with no sound (enemies dying, getting hit, other assorted stuff)
3- Something came to me. Shouldn't we be helping LIBERATE the fungi? If so, why are we killing every mushroom in our path?
4- Movement is a little problematic. You get stuck on walls, which makes navigating more difficult than it should be. You should make sure that when someone is moving diagonally against a wall they don't stop moving and just move to the direction where there's free space. For example, if you're moving to upwards-right against a wall above you, you should still move right if there's nothing there.
5- Shooting only at the direction you're facing makes attacking some enemies while dodging their attacks (like the saucers) fairly difficult. I'm not sure you prefer it this way, but perhaps you could experiment with using WASD or something similar to attack in any of the four directions, regardless of your movement? This might be too big a change from what you were planning though.
6- If you're going to be adding quests, please try to refrain from "Go here and kill X enemies of Y type", and assorted fetch quests. It's been done to death and beyond. You could do stuff like "There's a strong green alien mistreating all the fungi over there", and that leads you to an unique boss fight, or have you find and collect unique items, and so on. You don't need many side quests, you just need good ones.
7- There are a few typos on the story screen.
8- Advancing the text on the story screen is very problematic. The text is written at a very slow pace, making me have the urge to speed it up, but if you try to press space it skips the whole thing, and if you press down to make the paragraph write instantly, it'll automatically skip to the next one right after, making the only option to read everything at a slow pace. My suggestion is to do like your average RPG, where when you finish showing a paragraph on screen, it stays there and waits for user input to continue, and if you tell it to write faster it will give the player time to read and not just skip ahead. Also, remove the ability to skip the whole scene, or put it on Esc and not on Space, or else you'll have a lot of players skipping the whole story accidentally.
Overall I'm really liking what I'm seeing here, and I hope you continue expanding this.