I always preferred Quake. I still play QL on rare occasion with a couple of buddies when they invite me.
Eternal was pretty good and was I think the peak of the Doom series. It's hard to say any of the games were bad. But I don't really care to play them that often anymore.
Quake always had the better multiplayer, more interesting albeit less polished lore (my opinion), more interesting level design, better gunplay and so on. It's a shame that Saber decided to just shit out the moderately okay Quake Champions and then let the franchise rot. But we have Warfork and Xonotic now which have small loyal communities and everything I liked about Q1+Q3 so it's not all dire.