Digimon would still kick Pokemon's butt in a fight.
In fact, the power difference has only gotten bigger with time. Basically Arceus (being God and all) and Dialga (depending on how much control over time you believe it has) are the only pokemon that might stand a chance against a Mega-level Digimon.
Also there's now 6 seasons: Adventure, Adventure 02, Tamers, Frontier, Data Squad, and Xros Wars. Of these, Xros Wars is the only one that hasn't aired in the US. That will be rectified later this year, as Nickelodeon has agreed to air the localization of Xros Wars, which is being renamed Fusion.
"My faith protects me. My Kevlar helps." Michael Carpenter - Death Masks Official Norn of the Shin Megami Tensei IV board