The first thing is that the controls felt very awkward to me with WASD to move and X to shoot, since that's what the instructions ingame say. Especially in a game where I feel very heavily incentivized to be shooting constantly in order to tell where I am relative to the walls - which feels like its own problem. This gets compounded by the fact that there's no autofire holding down X, meaning my right hand was just stacked underneath my left hand mashing the button constantly. There is also no cooldown for firing, meaning that you can just mash as fast as you can and fire very quickly. I only realized after my first playthrough or so that space would also shoot. I felt a little foolish, but the instructions ingame should probably say that X and Space will both shoot.
Back to the "shooting to tell where I am" problem - it does not feel clearly communicated to me where I am relative to obstacles. Some enemies or obstacles can feel like they come out of nowhere since the camera angle doesn't let you see very far forward at all. This is a lot worse if you're specifically in the upper right corner. The section with waves of hornets I entirely gave up on shooting them and just mashed the fire button in place, since it was a much safer option and I could not reliably aim my shots to hit anything. Without walls, there's nothing my shots can consistently hit, which meant no way to tell exactly where I was in space.
The boss enemy exacerbates the mashing problem, since to kill the boss faster you just mash as hard as you can, look at where the bullets hit the boss, and then use that as a reference for dodging the attack patterns, then alternately move in any direction to dodge the attack that fires towards your position. With quick enough mashing the boss can only get in a few attacks.
The flowers that fire sideways also seem a bit awkward - I was never threatened by them, since they always fired way ahead of me in a spot where I couldn't possibly be, and then didn't seem to fire again. I'm not sure if it's possible to get hit by the projectiles those shoot.
The pollen system as well didn't feel very consequential. I was able to beat the boss without ever shooting a flower, but keeping your pollen topped up is generally pretty easy anyways.
I'd also like to note that the height meter on the side isn't very helpful, and in my opinion misses why the height meter in the original Zaxxon was important and useful - in Zaxxon, the height meter is oriented on the same plane that the ship moves on, with bars on the meter which correspond to the lines along which the ship is controlled horizontally. This, especially in the indoor sections where the wall is also easy to trace relative to the height meter, makes it much clearer where the ship is in the physical space of the game, as I've tried to illustrate below
Without the meter being exactly relative to the space, alongside height markers angled for perspective grounding the meter in physical space, it becomes much less useful to the player for determining their vertical position relative to enemies and obstacles. The provides clarity - you know the top of the high section of the wall on the left side goes to the top of the height meter, so you can also tell about how high you need to be on the height meter in order to clear the rest of the wall at a glance. The Beexon meter, though, doesn't directly correlate in this way, so it doesn't cement the player's
I know that this was kind of an essay, but I hope this is helpful critique for you. I love these kinds of modern adaptations of old retro games, and I love the character of this version of the game - especially the little frogs