Man there's a lot to love on this one.
Great vibes between the stage design and enemies, and just general feel and design of the game as a whole.
Excellent job on all the custom assets, especially love the 3D models!
I have to agree with some of the other comments that a checkpoint before the boss would do wonders, especially in the later stages where you're constantly dealing with enemies from both sides, it can get tedious to have to play through the whole mission just to get tossed around by the boss and lose.
In a similar vein, I think a boss rush mode would be an awesome feature, to let you practice the fight themselves, then take that experience to a stage and try to shoot for a high score!
It would also let the player explore the other characters a little easier in a space where you really want to make the most of their abilities - I only played as Amelia cause I didn't want to restart from the beginning and lose my progress to try another character, mostly due to the fear of not liking them and losing my progress.
But I think the stage, enemy, and ability design are great for encouraging the player to use all of their tools - there are many scenarios where you need to combine time stop and your ability to make it out unscathed, but with them both having relatively short cooldowns, it doesn't feel overly punishing.
A couple of things I saw that might be bugs, so I want to bring them up here - I noticed the jailbirds would occasionally propel themselves off screen with their attacks, and sometimes would still keep firing when I couldn't even see them. And with the way the timestop recharges, you can just hold down the button even when it runs out, and it will immediately consume the charge when it refreshes, causing enemies and projectiles to kinda skip around. Wondering if you could try preventing timestop usage until it reaches 50% max when it fully runs out to help resolve this. Or maybe its not an issue at all. Also I think the Kronie projectiles weren't affected by timestop (I only payed enough attention to notice it once, every other time I was busy trying to avoid something else and couldn't tell), which makes sense for their character, but it is a little inconsistent, since I think they're the first enemy to do that and it's not communicated that that's something you need to look out for until it happens and you notice it.
But really that's just me trying to be as thorough as possible, overall great submission. Fantastic work!