Hey, PHI, thank you for taking to record, analyse and comment Sipho. I wanted to watch your video in full focus before commenting, sorry that it took so much time.
I believe that the damage to controlling player caused by "physical correctness" we are aiming for can still be mitigated by programming movement controls more smartly. Although I would agree that the subtle differences and benefits of movement parts are too subtle to feel impactful and at certain player size / movement part count it becomes negligible. Assuming new player has enough patience to reach that far.
Struggle with controls you've experienced is a combination of new experimental physics we haven't accounted for (overshooting) and old assumption of constant "turn ratio" which causes movement logic to always prioritize turning, hence you not being able to strafe with your movement setup. "Bad movement" is now a common theme we get in negative reviews and refunds we must fix.
There has also been a hilarious amount of powerups you've picked up and I should somehow balance those - so many that they stop making a difference in your actions. That works against their design goal of encouraging player to change their current strategy (flee -> defend or defend -> go on a frenzy killing everything).
The issue with powerups is also the issue you mention with picking up new parts - I'm slowly working on coming up with new synergies between parts so there's never a "meh" pickup option of the boss drops and every pickup should provide a significant boost to the player's build.
I feel that my "conservative game design" can be felt though current insignificance of mostly any pickups and the buff powerup of powerups. I've been designing this game too much as a balanced multiplayer game and not enough like a crazy single-player experience. One of planned features to mitigate this are passive buffs called "Mutations" that can be exclusively picked up among Zooid drops - so you can either choose a new zooid or permanently change stats of your current and future Zooids. You could consider them as Zooid upgrades you have proposed.
tl;dr; I should be less conservative with power spikes and make them significant and guaranteed. Movement will be fixed, sacrifices will be made if necessary.