For all factions, it will be beneficial to upgrade everything that increases movement speed, such as speed aura and tactics. This will allow you to reach the invisible units faster. Sharp Mind is also useful; when a hero moves earlier, they can somehow help deal with the stalkers, cast a mass speed spell (some ranged units attack before the enemy), or teleport someone.

Now, let's look at the factions.
1. Humans have griffins that can attack stalkers from the sky, but this requires careful planning, as a smart opponent will simply move the stalkers instead of using invisibility. It is useful in this context to split the griffins into a couple of stacks (if possible) and deploy archers that will finish off the "revealed" stacks.
2. Mages have it the easiest. They deploy obsidian golems and forget about hit points.
3. Orcs can do something similar. When deploying troops, shamans and centaurs are split into 2 stacks. Shamans usually move before stalkers, slowing them down or speeding up the centaurs, so the centaurs also move before the stalkers and partially solve the problem. At least, they speed up the solution.
4. The Elves have an initiative-based army; many units move earlier and probably won't allow the enemy to cast more than one spell.
5. It's a bit more difficult for the Demons... But here you need to rely on levels 3 and 5 (they will reach the enemy quickly), as well as level 6, which has area-of-effect spells.
6. It's probably even more difficult for the Necromancers. Nothing comes to mind right away... Let's see what people can say about them.
7. Gnomes often encounter Chaos, so the "fireball" and "meteor shower" method will be appropriate. In any case, there is a speed rune; use it and find the invisible units quickly.
8. The Warlocks themselves also search for enemies in Chaos and rely on dragons, furies, and lizards, as well as assassins, who can move earlier.

Added 3 minutes ago
I think that in 3.0, Warlocks won't trick Mages. The new golems are a terrible threat to them.

Added 2 minutes ago
I completely forgot; Necromancers (as well as Demons) can have the "Unholy Word" spell, which will kill all stalkers.