The .22 caliber is better coyotes, while the .25 is better for deer. When using one gun for both hunts, I generally err on the side of bigger diameter. In this case, I wouldn't want to use a .22 caliber on deer, so I advise using the .25 caliber.
Any particular reason why you are set on the .25 WSSM? You can get the regular .25-06 available in many more makes and models, not to mention factory loads. Now, if the .25 WSSM was in a .25 WSM make, meaning velocity higher than .25-06, and just a bit lower than .257 Weatherby velocity, then I would opt for the .25 WSM. However, Winchester made it only in a WSSM form and, as such, I would stick with a .25-06.
Zachary