Ok, now that I've the hatched polygon figured out, I can try solid planes. I will check out naming the pads/vias as well.
I had vias in both thermal pads, will check & see what happened to them. I might have just turned viewing them off when I did the screen captures.
There were a few pins that couldn't connect to the ground hatching because there were too many signal runs in the area. I had to run a trace by hand, adding vias to bring the signal under the part and back up to where there was a ground signal to hook up to. Just a little too complex for the autorouter.
I think part of the reason for the ugliness is the shield footprint. The placement of some signals is just poor, and the size of the 1284 means you can't cram everything all in the same spot.
Skyjumper just had some similar boards made (little bigger more connectors), the bare PCBs look good, I think I'll follow his lead as he's nearby (Boston area also) and they were made & returned pretty quick.