Thank you for your very detailed comment! Definitely the deadline affected many of these elements.
There are actually player shot hit effects that exist but went unimplemented (also didn't get to make/get a handful of SFX, including player shot hit). Never planned for a bomb mechanic but I was going to add powerup pickups, and also considered having a special attack tied to the timer (which also went unimplemented), so it'd dry down the timer in exchange for big attacks.
I did get some complaints while devving about the enemies looking like they just magically disappear due to the way the explosion worked but we didn't consider just making it bigger, I'll take that in mind, maybe spawn several if making another or multiple explosion anims is too much.
As for the hitboxes not sure what to do. The player shot hitbox takes up a bit more than the whole sprite while the enemy bullet hitboxes tend to be a little circle in the center, felt fine to me but they're definitely not that well thought out.
The stage design and layout is the result of putting together ended some patterns I had + some new ones I had to make while dying of stress, all the day before the jam ended, so definitely some of it might feel pretty haphazard. I'm planning to rearrange it into something more sensible for the update. I would have liked the music to guide the stage design as well but didn't have enough time to properly think that out. I also need more time studying other games, had never done that before this jam.
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Multiple explosions that cover up are the way to go IMO, they always feel quite good.
I think the enemy hitboxes being so small is the problem, you wanna separate the enemy body hurtboxes and hitboxes, making the hitboxes small while keeping the hurtboxes quite large, this is the best of both worlds.
Enemy wave design is tough yeah especially on a time limit since you don't exactly have the time to do a shit ton of playtesting to make sure it flows great, but well that toaplan left to right to left pattern never fails