I am completely green at using Linux, although I did just install Ubuntu 10.10 so I can learn more about Terminal commands and file structure, which I guess are shared with the Android OS as well. The only thought that comes to mind from what I have read is that newer versions of Linux distributions use EXT4 formatting for their files. So I don't know, for those who want to interact their Ally with a Linux PC, whether there might be any benefit if both devices had the same format on them. Aside from that I agree with your thinking. Unless I learn differently I plan to leave my SD card as EXT2 as well.
Zoandroid