I don’t know if anyone has already mentioned any of these before, I would like to share this sentiment anyway.
I don’t like that thylakoids produce glucose; because carbon fixation is done by RuBisCO - which is located outside the thylakoid. Instead, it should be an ATP generator just like metabolosomes and rusticyanin are (only that it harnesses the power of sunlight unlike the other two). That’s what thylakoids are in real life anyway; just that, in chloroplasts, the ATP generated is immediately spent on RuBisCO to make glucose.
I’m also not a fan of “prokaryotic structures” in general; they’re just a collection of proteins anyway - with the exception of thylakoids of course - and it kind of ruins the immersion to see, for example, clusters of iron minerals for rusticyanin, and whatever that thing is supposed to be for nitrogenase. As far as I know; rusticyanin is a protein found within the periplasm (the space between the inner and outer membrane). Though I saw an image somewhere in this forum that suggest that this will be changed in a future update (where they are in the “protein collection” instead and the only visible structures left is the thylakoid and probably BMCs like carboxysomes as well).
Edit: I’m just gonna expand on the “prokaryotic structures” bit. I’d like to share this:
It has references to 30+ scientific papers btw. So instead of basing the cell structure on component placement; you tune it to the ratio of different structural proteins. Complementing to this as well with surface structures; where cell movement can be influenced by its’ shape as well as the flagella’s placement.