"it's less confusing if the analog pin indexes match up with the digital ones"
I wouldn't think so - A0-A5 as D14-D19 has been the "standard" for quite a while now.
I would find it more confusing, and hurt with backwards compatibilty, if D0/D1 were not the main serial port, if D11-12-13 were not the SPI port, if D18/D19 were not the I2C port, etc.
"Before I decided to upgrade my design tot he 644P or 1284P"
Your kickstarter page does not mention that (yet?). You appear to have planned this project out pretty well.
The room for larger sketches & SRAM offered is nice. I have used the extra IO offered vs adding another chip or two to a project as well.