The answer is simple. Shadowrunners are covert operatives operating in small cells, whose main benefit for the employer is deniability. There is also a large number of world-class professionals among them, and often at rare skills. Thus, they should be used for the tasks that utilize those benefits the best; and it falls to the GM (and to a lesser extent to the writer) to find something for them to do.
I've actually written about this in Yuakut Shuffle, cause finding stuff to do for the runners on a battlefield is basically the same issue as the one at hand.
Runners scouting out the enemy beforehand? Sure. Sabotage, assassinations, taking POWs to be interrogated - all tasks for a shadowrunner troupe. Frontline combat is not, because if you try to maintain any semblance of believability, it becomes very random and very deadly. Standing anywhere near multiple Great Dragons engaged in direct combat is always a bad idea if staying alive is a part of your plans! If you want your runners participating in the "final battle" that badly, fine, give them a SAM installation or an artillery battery to control, or a small unit to command, or, hell, at least use them as long-range snipers and mages. Perhaps give them a LAV or something to buzz in and back out without dying. Just don't have them charging a Great Dragon with melee weapons over a fragging minefield (which is now
canon)!
That said, I find the very idea of Great Dragons fighting a full-scale open war rather distasteful. Great Dragons are immensely powerful beings personally, alright, but their influence stems not from their personal power, but their intellect and wealth. Why is their war fought openly, rather than behind the scenes, precisely where the runners thrive? That'd eliminate the problem altogether - leaving, perhaps, a slight issue with the very final showdown, but I can't exactly remember the Golden Snout dueling with Nachtmeister personally or an interceptor wing shooting down Feuerschwinge raising any protests from the players that they didn't get to participate.