Is there a reason for doing it without a matrix? (just for fun is a good enough reason
). It'll be more painful to route for no particular gain. You could then use a smaller MCU.
1: I'd recommend to check the datasheet for the ESD protection-chip you plan to use, implementation can vary slightly. Most often, you just connect the D+ and D-, VCC and GND to the ESD IC that sits in parallel, but some sit in series, so make sure to read the DS. Placement should be close to the connector and protect the traces between connector and MCU.
2: USB is not a bus, so you can't connect a second device to the same data-lines, you'll need a internal USB-hub or multiple data-lines (like multiple cables) to get pass-trough. Since you are using a USB connector and not a dedicated cable (that could split into two at the PC side), I'd go with a internal hub.
I'd also recommend to change voltage regulator to a more modern one and reduce the capacitance of it's decoupling caps. Ideally, you want to keep your total capacitance for a downstream usb-device to below 10uF.