My preferred method with soldier is to be on their flank, preferably near a corner or doorway that allows you to play peek-a-boo.

The idea is to chip away at Mercy as quickly and efficiently as possible while ducking in and out and watching Pharah in your peripherals. I'm sure I'm preaching to the choir here, but if you really focus for a second you can burst Mercy down almost halfway in an instant using one or two bursts to the head. Then duck inside while keeping tabs on where she was headed in the sky. Then peek back out before she can start regen, and you have a pretty good chance of already knowing where she could be, so open up again and if you get enough headshots you can hopefully kill her at this point.

If she's being a pest with her flying around it might take me one more peek, at which point Pharah probably knows I'm there. So I put down bio field and open up on Mercy without the peekaboo games to finish her off. Chances are at this point in the battle they might be closer to you so you can use rockets with a little luck just end it quickly.

Once Mercy is gone you can deal with Pharah as you see fit. I like to sprint to the nearest defensive spot and do basically the same thing to her from there. If she doesn't die, at least you've broken up their strat for the time being.

It's mainly about predicting where that Mercy is gonna be as she's flying around so you can stay mentally one step ahead of her physical movements. Also using tall walls so you can kind of ideally keep Pharah out of your LOS while still shooting at Mercy. You can be a pain in the ass for a long time if you do it right and Pharah will have to come hunt you down to stop you.

This might be an extremely rudimentary method of dealing with them but it's never gone wrong for me yet. And if I didn't explain it very well I apologize, I've had a couple beers. :)