Yes, but: the initial design could not autoroute. I then did a manual route and solved many of the issues by moving components, and ended with ugly looking traces at funny angles & stuff (routing with laptop finger pad is not the best way to go). I was able to get that to autoroute with a couple more small moves and only had to manual fix up 3-4 traces, so the traces ended more or less like my manual version but much neater looking. Eagle maintained the clearances and selected the drill sizes & stuff so the errors were limited to tStop & tCream overlaps, which some sliding & scooching around resolved.
The same approach is not working so well here with the FTDI chip, the SD card driver, the RS232 driver, all of which the other also had, but also the RTC, smaller board size, jumper fields for user signal manipulations, etc. I had the manual routing done, looks like a checkerboard pattern, but it won't autoroute. Also want to incorporate your suggestion on the square pads vs round.
I haven't looked at the international circuits Design Rules yet, not sure where that will lead.
Solution might be to widen/lengthen the board, have the atmega placed closer to the digital header pins and move the support chips to the 'analog' side of the DIP.
I still think the original shield pin assignments are part of the problem, with signals criss-crossing the board.