Having played both Marathon and Doom at the time of release, I felt that Doom "felt" a lot better than Marathon. Marathon always felt a little too clean and polished and bright, and the weapons didn't have the heft that made Doom so much fun. Funny thing is, Marathon followed the "rules" of good game design better than Doom (it was making them up as it went along actually) like plot, variety, immersive enviroment.
But I think anyone who loads these up today will still say that Doom, for whatever reason, is still a hell of a lot more fun. Maybe it's the shotgun