Yes, I believe so. I am not sure the exact solution in your project, but some sprites like the character are aliased making them seem really blurry. I always try to avoid this when using pixel art, its a pretty common issue.
For the difficulty, its hard to give an exact answer, its just something you will have to iterate on. I would start by maybe making the base enemies a little more difficulty, and have their upgrades scale less. It feels right now like the enemies are 0 threat for half of the time I played, until the upgrades really started to compound and they became way too strong.