Troubleshooting: Is there a way to change the size of Cross Section Annotation?
There isn't really a way to change the size before it is placed, but you can modify it after it is placed.
When creating the annotation feature class you can set a reference scale. If you choose a reference scale of 1:1000, your 12pt. font will be displayed as 12pt at this scale. So you can change the reference scale of the annotation feature to place bigger or smaller depending upon the scale.