A SmartConnector is much much more than a Template. If you are planning to use and integrate two applications in a standard way (and assuming you have a SmartConnector for those applications) then it is always best to go with the SmartConnector.
With a SmartConnector the integration will receive bug fixes, new functionality and settings. It will have documentation and specific domain support, etc… all the basics that come with any other fully managed application. In contrast, Templates get none of that. A Template will have a lot of the same initial integration functionality built out, but once a template is installed, you can do whatever you want to it.
All the managed components belonging to a SmartConnector (that are locked from being changed -- to preserve the ability for the SmartConnector developer to upgrade them) are completely unlocked in a Template.
If there are no SmartConnectors available or if you are planning to use an application, or integrate two applications in a non standard way, then a Template can be a better choice.