Would've done this as a quick PR, but alas, my KiCAD's too new, doesn't allow me to save as your file format :(
So, here's what I'd change:

Looking at this, the via between C3 and the FTDI IC is probably superfluous / ill-advised; I should've moved C13 closer to the IC.
The 12 Mb/s USB data lines aren't very fast, so I presume that the coupling when routing them below the other line (R3) isn't that bad.