Nice game you have here, I look forward to see how it evolves.
Now on to the feedback:
1.For the love of SWEET BABY JESUS, stop spawning enemies out of nowhere next to the player.... It's really annoying and gives the feeling of an unwelcome element of luck that can cause you a premature game over with little that can be done about it. If you still wanna do that then do it off screen, or make a visible, delayed warning sign like bosses do.
2.The zooming distance is a bit small compared to how easy enemies can ambush you. Getting jumped from behind by a second enemy is pretty shitty.
3. Some parts differ only in appearance, the connectors are a good example. Maybe tinker the stats so that different zooids from different species have different stats. Example: species 1 connector: 1 and 2/ species 2 connector: 2 and 1. Same for all other parts, different stats to make the races more interesting.
4.This is just an aesthetic, but changing the color scheme of a zooid of another species to the one of your own core/species would look better than making a frankenstein creature like you do now.
5.An armor block zooid? A plancton collector that generates nutrition over time? A directed shock emitter that disorients enemy zooids? A pheromone zooid that pacifies enemies for a short while? A storage unit that is heavy and frail but holds lots of resources?
Think outside the box, don't just have connectors/movers/weapons/mouths.
6.The Ai is good at pursuing and running away, but clumsy at avoiding terrain and untangling creatures from one another. The bosses are pitifully easy because of this.
7.Optimize the game pretty plox. The frame rate can suffer near multiple whirlpools/large number of enemies/very large creatures like the box fortress beasts in free roam.
8.The ui and menus are really bland compared to the rest of the games aesthetics.
9.The music is chill and nice, a good direction given the games nature.
Thats all I can think of right now. Good luck and keep at it.