Thank you guys for the interest and the suggestions! I will try to respond to a few of them here:
"I have occasionally thought that there should be a niche for a similar board, but with on-board stepper drivers (Trinamic or some other serially-controlled driver)
That would, of course, need a dedicated HAL driver, but those can be surprisingly straightforward."
I was actually planing on designing a seperate IO Board featuring the Trinamic 5160 Drivers, as they would allow me to run high current stepper motors. They come with UART and SPI interface functionality but I haven't really seen an advantage in interfacing them serially. Maybe someone has a good argument as to why it would be worth it to go through the integration troubles?
"I like having the boards seperate, just in case my butter fingers cause one the voltage translation chips to blow a smoke valve and damage the PCB."
That was my thought process as well. I'm a little hesitant to put everything on one big PCB, as i feel like that would make errors more catastrophic. I also like the modularity of having seperate PCBs, especially in these early prototyping stages. I did actually bring the JTAG out, but realize that better labeling was neccesary, which I've since added.
"I am liking the look of this board. Did you do this in easyeda?
Suggestion, add the rpi 40pin header. Aside from being able to add stuff rpi side, I find it valuable for debugging the MCU/FPGA side of the board using a regular rpi without having to keep removing a cm module and you can use it as a backup incase you damage the 100pin hirose connectors or theres another RPi/chip shortage"
Yes, I did do this in EasyEDA. I started the project with EasyEDA becuase I foud the integration with the JLCPCB services appealing.
Including the 40pin Header is a great idea, which I will definitly add. Unfortunatly that will require major rerouting. Before rerouting everything I will continue collecting and thinking about additions/optimizations. That way I'll hopefully save money on design itereations.
I'd love to here if you guys have any other sugestions. The design philosophy behind this board is to make it the Compute Module 5 version of the Mesa Electronics 7c81, and I will probably finish this project making exactly that but I'm also open to brainstorming other ideas for potential future projects.
Thank you everybody!