Looks really neat!
Since you are using 6p6c connectors and duplicating the VCC and GND lines, it would be better to switch the positions of #2 and #4, in order to follow the wiring pattern advice in the I2C-bus specification and user manual (UM10204), Chapter 7.5. This will also make it compatible with the current version of the Hub (at least midly compatible, there's still the ENABLE line in the middle). By the way, regarding your question about the Hub in the other thread, send us an email to contact at chordata dot cc.
In the last revision we have also added an i2c buffer (TCA9517), I merged the branch to master so you can take a look at it here: https://gitlab.com/chordata/PCBs
It is not absolutely necessary, but would improve the bus stability under long cables.
You can drop
JP2 if you need some space. They are just there to ease prototyping, allowing to bypass
U2, and sometimes used as testpoints.
Looking forward to see this working!
And remember: Since you are basing your development in open sources, it is a good practice to keep a public repository (or online folder) of the work you are doing from the beginning, and include the open hardware logo somewhere in your design.