Same remark about pads applies to USB receptacle - those micro and mini USB SMD vesions are hopeless for PCB
Use THT version if you want that to last longer than one insertion. Or preferably use angular USB-B (beefy ones as in USB printers).
The blob on a negative CR battery contact is not a good idea as it might short the battery while inserting it. Just make pad bigger and also make sure you won't scratch soldermask and short something.
As for NRESET - that looks ok but you would have to disconnect FTDI while debugging/programming as there is a capacitor involved.
The AVCC is shorted to VCC and that is not what datasheet recommends.
There are vias under TQFP - not sure about you but I always etch a PCB and test it before I order a final version. Drilling and soldering vias under TQFP is PITA. You can usually overcome that with ugly jumper wires but I always try to move via "outside" first, if possible.