As far as I know, there is no OOTB capability to define which template is your "prefered" template. It's not the same as the default doc type preference because there would need to be a preference created for each available document type. If you are only using one type, this would seem to be fairly simple. With many subtypes, you can see how it would get more complex.
This request has been logged in the backlog and PTC plans to address it in a future release, but nothing has been confirmed yet. To keep it moving, I would suggest creating an Idea for it so other folks can vote it up and help prioritize it.
If you have a critical need to get it implemented now, I would suggest creating a custom "New X Document" action in Windchill where "X" is the template you want initiated. Not being a customization guy, I don't have a good reference for you other the Windchill Customizer's Guide available as a Reference Doc on www.ptc.com.
Any other ideas?