The "scaled shorts" format (hardly original with me) is not to save CPU time but to save disk space and memory space when a time series is read in from disk. These considerations were important back in the good olde days of the mid-1990s, when AFNI first started.

I'd consider make the default output format for the various programs be float, but this might break some scripts out there. I'd like to hear some debate on the issue before making such a non-backwards-compatible change. Generally, I like to keep the software's default operation mode be the same, for the sake of all the users out there who have their standardized ways of doing things.

In some cases, I have made such changes that break consistency. For example, when I discovered (in Nov 2006) a logical error in the way 3dFHWM used the -mask option, I fixed that -- which meant that the results of this program would not be the same when run on identical inputs (that is, the before and after the program versions would give different outputs). I flagged this in the -help output in case someone would get confused.