I have to say, that if it's late Genesis vs. early Marillion, early Marillion is the winner hands down. I love Duke, like Abacab, love the first side of Shapes, like Domino off of IT, and like DTLS and Fading Lights off of WCD; I did really like Calling All Stations, even if it did sound like a cross between Bankstatement and Mike and the Mechanics. On the other hand, I love Script and Fugazi, and CAS ranks as one of my favorite all-time albums. MC was o.k. I liked some parts of it. And Hogarth-era Marillion was good too up through TSE. Overall, I would say that Marillion was producing far superior work in the 80's than Genesis. Of course, early Genesis vs. early Marillion would be a whole different ballgame.
My vote goes to Marillion.