Hey Psi, sorry to see a lot of criticism on a project you have worked on for a long time. I know the feeling, but it is good to see you are willing to make changes to improve it. I'm sure it will be for the best.
Everyone has their own opinion of course but I like the original graphic style and think you should stick with it. The 80's comic book look is your point of difference, if you redid it with proper pixel art you would lose the nostalgia aspect and the heart of the game imo.
I won't nitpick, but there are 2 big issues that stick out when i watch the video. The first is the screen size.
As a beat-em-up game, I personally would like *at least* this much extra space on the screen to be able to navigate through enemies and plan my moves instead of just reacting to whatever pops on the screen (might need to widen the browser a bit to see the full image).
The second thing is how your hero carries herself (pose and animations). You can tell a lot about someone by the way they stand and move. Most of the time she is slightly bent forward which to me portrays anger and generally isn't a flattering position for her. Why is this important? Well, this is very sexist but I feel like she should move more elegantly/gracefully. To be more specific, she should move in poses that accentuate her features and make her look sexy (especially since she is outfitted with a skin tight costume instead of armour that is designed to be functional).
Straighten up her back to have her in positions that convey confidence. When animating, it might help you to select a strong pose like an attack position (the point of impact for example) and work backwards bringing her to the idle position. Change the running animation to a walk (keeping the back straight for the majority of the cycle), this would suit the speed she moves at much better in my opinion.
Again, all just my opinion, for the most part I think you have a great project and wish you the best of luck moving forward.