Please change the default server selected when you use New -> Server for the first time.
In JBT, this should be WildFly 8
In JBDS, this should be EAP 6.1+

Also, see Max's comment in JBDS-2915:

Currently that is set to AS 4.2 !?
https://github.com/jbdevstudio/jbdevstudio-product/blob/master/plugins/com.jboss.devstudio.core/plugin_customization.ini#L54

It seems you should be using this to customize it for JBDS. Instead, you override this using some other mechanism.