Honestly, page-based systems that can be accessed with a castle/boat switch is fine for modern fighters and trained pilots. Hearing a trained Eagle driver rattle off how to get to a specific menu/page from any other page is pretty impressive- "You need to change missile mode but you're on the ECS page? Back, down, down, right, right. [or something like that]" And they aren't even sitting in the plane or looking at the screens, it's just muscle memory.
Non-military specific, and the biggest con of touchscreens in a cockpit: - Turbulence makes it hard to hit the right places on the touchscreen. Traditionally you'd rest your hand or stabilize a few fingers on the outside of your radio/navigator before twirling the dials or pushing buttons, and there was enough resistance to keep from accidental presses. With stuff like the GTN 650 pushing the screen out to the edges, resting your hand on the bezel means you accidentally make touches to the edge of the screen. Competitors like Avidyne actually market old school buttons as a feature, and it's a compelling one.
Military specific concerns: - Wearing gloves while flying means that button size needs to be huge and touchscreens aren't very precise. - High-G maneuvers make it really hard to touch the right part of the screen.