Currently (v2.5), you have to manually launch escort crafts from same base or nearby bases and manually manage rendez-vous and courses so that a transport is no left alone for too long. Moreover, the crafts don't adjust their speed to each other.

What if, on clicking on any armed craft, you'd have a line "Escort Transport X" for every transport (X,Y,...) flying, and at range. Conversely, on clicking on a transport (armed or not), you'd have a line "Ask for escort" that would in turn pop up a new window; akin to the Anti-UFO Defence window, listing all the craft currently at base or in mission, so that you may chose the one that would fly after this transport to escort it.

* An escort mission would last until escort craft has too few remaining fuel, transport lands to base, or the escort craft is manually detached (Stop/Return to base/etc.).
* The escort craft would first "intercept" the transport, then follow it at same speed in a parallel course.
* If the transport is manually managed, this would not hinder the escort craft (only managing the escort manually would abort the escort mission).
* If the transport drops soldiers on the ground (player entering battlescape), the escort craft would just wait on the geoscape, and the escort would resume when the transport takes off.