I usually am really bad at these types of games but this one has been rather fun, though challenging in some parts. I've thoroughly enjoyed my plays of this game, and I think I've gotten to the final boss of this release, however I'm not sure. The checkpoint system is fair and not spread too far apart or too close to each other as well. I like how there are different characters to go along with various play styles, too.
The first issue would be that the controllers don't work well yet, however it's likely due to me having a DS4 and it's not fully implemented yet, if I recall in the readme. That's just a minor inconvenience though, and I'm pretty sure you're aware of it. The main problem is being able to go through walls (specifically corners, which you can see pretty early into my gameplay I'm going to post) and falling through the world. Second issue I noticed is you can "cheat" the water by jumping up out of it and holding down to technically swim under but it acts as if you're floating on the surface. That could cause some problems other than cheating, but I'm not 100% sure. The next thing is that I feel that the game, thus far, is a tad too easy, granted it may be that way only for the pre-alpha release, and you intended it that way.
I'd say, in my opinion, that increasing the difficulty (not in general, but with the gauge) would give the enemies more health as well as hitting harder, or smarter AI tactics. Just don't spam enemies, which from what I've gathered, you do know not to. I liked the idea of "hoards" that come from the air ships at random places, that was a good step in challenge. If you chose to go the path of increasing the health of enemies with difficulty, be sure to not overdo it for the "hoard" enemies from ships. Another thing I might suggest, for those with multiple monitors, is a mouse lock option where the mouse cursor stays in the window. I was having problems with not paying attention to how far right I was moving my mouse and ended up tabbing out when trying to shoot.
Overall, as I said, it is a great game so far, I'm definitely looking forward to more updates.