Great project as always.
I could definitely see your balance changes to the first stage, allowing it to lean more towards the reactionary and less towards the memorization (though memorization has it's own dedicated fanbase of course).
Powerups seems to suffer from a screen coordinate lock that is completely independent from the actual background. What this leads to is a powerup that spawns in an obtainable position but then ends up in a wall or floor or ceiling because the background has scrolled up or down and the powerup hasn't changed y position to compensate (this was all Stage 1 issues upon entering the ship.)
I enjoyed Stage 2 for the most part and it absolutely gave the impression of a city under siege but a lot of the time the enemy waves felt extremely chaotic (sometimes in a good way, sometimes bad) and it started to lean back into the memorization camp of shmups. This isn't a bad thing though, because stage progression should be harder, but the jump from what you made Stage 1 into with your rebalances going into Stage 2 is almost jarring.
Again, great project and I look forward to seeing where it continues to go!