I think you're on the right track!

I've been designing this game too much as a balanced multiplayer game and not enough like a crazy single-player experience.

Yeah, this is something I call symmetrical game design, where the enemies have the same power levels and follow the same rules as you do. Some devs seem to be drawn to this kind of design, and it definitely has its benefits in the kind of game feel it can provide, but also has downsides and design challenges it introduces. There's a number of stuff that works better with the freedom of asymmetrical design. An example would be in a traditional shmup, having the player bullets move fast and the enemy bullets much slower is a dramatically better experience than if the dev followed some self-enforced rule about how all projectiles need to be the same velocity because that's what "makes sense." I think you have the ability to strike something of a balance. You could keep a lot of the consistency in how parts work between player and enemy but also find certain ways to inject boosts to the players abilities to empower them further. 

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.

I'm not sure how into this I am tbh. For one thing, it's a bit weird to give the player a choice between an upgrade and a sidegrade. Wouldn't they choose the upgrade each time? Sure there is *some* value to diversifying your options but I would find it hard to justify that over making my existing abilities stronger and more compact. You might end up balancing this choice by making the upgrades quite weak overall which also seems like an unfortunate solution. 

I think the idea of being able to spend nutrition to upgrade existing parts is much better. It's intuitive and satisfying to the player, and it functions directly (in the build mode) in the area of interaction between size and power of the player. It's a common element in things like tower defense games, where there are spacial limitations at play and it's impractical to simply keep adding more towers  so instead you can upgrade them, and there's some interplay there where you have to make decisions between adding towers or upgrading. I think this is something that is perfect for Sipho, especially since the idea of being small and nimble at least some of the time is very appealing but not often very practical for combat since you're so vulnerable. It's also nice to think that if you have put together a build that you like you can reinforce it further with upgrades rather than have to pull it all apart and try to rearrange and fit more pieces in to try to make use of your newly found nutrition (I found while playing the idea of ignoring newly gained food was often preferable to messing with a build I was already happy with). Lots of benefits to be gained from going down this route, I think.

The planned feature you mentioned could also work alongside this idea. Maybe the prospect of being able to upgrade new zooids you pick up would increase their appeal vs. the passive upgrades you mentioned.