I'd say in a crossover they'd need to have typings allocated. For example:
Agumon's line would be Fire type. Metal Greymon and War Greymon would be Fire/Steel, Skull Greymon would be Fire/Dark.
Gomamon's line would be Water type. Zudomon (who has Thor's Mjolnir) would have a secondary electric type, but Vikemon would be Water/Ice instead.
Patamon and Gatomon would be Normal type, gaining Fairy when they become Angemon and Angewomon.
Veemon's line is Dragon type, and Wormmon's line Bug type.
And so on. The Crests and Digi-Eggs would become held items. Having them would allow you to activate their Ultimate/Mega and Armor evolutions. It would work the exact same way as a Pokemon's Mega Evolution.
The plot could be that you're trying to defeat a virus that invaded the Pokemon Storage System, which transforms into a Digiworld. As a result, you wouldn't use Pokeballs. Both Pokemon and Digimon would be captured the same way as in the Digimon World DS games - collecting biodata with every enemy encounter. Encounter a mon enough times, you can create your own. Stats would be the standard Pokemon ones. Instead of stat boosting medicine, you'd be able to find equipment for the mons to use (weapons, armour) - another element from the Digimon games.
Certain Pokemon could have different evolution methods than usual. For example, a consumable item that activates DNA Digivolving could also trigger the Slowpoke evolution to Snowbro - it would merge with Shellder as mentioned in it's Pokedex description. Likewise, multiple Magnemite could merge to form Magneton.