Would you guys use an 8u2 or an 16u2 for own PCBs?
No. At the time Arduino switched to the 8u2, FTDI usb/serial chips were relatively expensive. Since that time, FTDI has come out with a cheaper line of USB chips, competition has appeared in the form of Cypress, WCH, and low-priced "modules", and the AVRs have gotten more expensive. On top of that, there are more chips with native USB (like the 32u4 used on Leonardo and Micro, or the SAMD21 on Zero) The 8u2 change to Arduino allowed the older design to have new USB capabilities, but those usually aren't needed. When they are needed, there are better solutions...