Stock (factory) bootloader in ATmega16U2
After some time working on another project, I decided to remake my PCB. I did some changes, shorten the traces, moved THT components on the other layer etc.

And it worked. My uC is recognized and enumerated as "ATmega16U2". This makes me feel confused, because my first PCB seemed to be good enough.

Thank you for responses. Now it's time to implement functionality, I'm going to use LUFA to make COM communication.