Well well.. I was just coming here to make the exact same suggestion..!
I have taken an interest in craft combat recently and one thing that struck me is the passivity of UFOS in the normal game. You can follow a large UFO around the globe with your tiny interceptor to see what it's up to and nothing bad happens.. That UFO is faster, tougher and has much more firepower, so it should just turn around, blow the interceptor out of the sky and then keep going.
It would also allow the transports' damage capacity to be a useful stat if they can be intercepted by UFOs (ex.: shot down by UFO fighters on their way to an alien base). That would be a further way to make the lightning relevant. It is much faster and much more resilient than a sky ranger, and can sort of defend itself with its one weapon.
A few mods already have the foundation for this with their fighters and it would be nice to build upon it with a new AI. The Interception screen would not even need to be changed that much. Once you are intercepted, you can still pick which stance you want to take, etc. The only difference should be that the UFO can move forward and back of its own accord. Forward to prevent you from running away or to bring shorter range weapons to bear. Back to keep you at bay and stay out of range of some weapons.
It would be particularly cool to give the UFO technology crafts the ability to back up from an aggressive UFO, trying to keep it at range, since saucers can fly in any direction, whereas the basic planes have to disengage and reengage if the UFO gets too close.
On a sort of related note: Is it possible to come up with a way to make access to the UFO stats sheets easier? It would be especially useful with mods adding new UFOs. Maybe something like: Every interception and recovery missions gives you a "Report: UFO X" item. Once you have a certain number of them, you can set your scientists to analyze the reports and the result is the stat sheet.