Changing programs used to launch an Application in Gnome3

Hmm, I misunderstood your question.

Changing the default terminal is currently not possible, because
desktop-entry-spec
defines no such thing, and glib refuses to implement non-standard
hacks
.

Since the codebase checks for several pre-defined
terminals
,
I guess the only solution would be to create a symlink from one of them
to your emulator of choice.