And saying Doom and Quake are better fps than X because "you can download hundreds of awesome crazy wads", is effectively the equivalent of saying "Skyrim is one of the greatest RPG's of all time because you can play Enderal instead"
Do you really think so?
Doom and Quake both have excellent foundation, that is their original content - weapons, enemies, items, mechanics etc. That foundation alone is better than most of everything that has been done since then, and on top of that it's easily modable, allowing it to reach even greater heights with the help of enthusiasts. Saying that Doom and Quake are better that other FPS is not the same as saying that Skyrim is one the greatest RPGs of all time, because Skyrim has shit foundation and any fan made content is built on top of that foundation. It's why many people say that you can't fix Skyrim with mods, because it's foundation is just trash, even Enderal is spoiled by it to a degree. Yet nobody in the right mind denies that Doom is a great game at it's core, and quality wads only improve something that is already good.
It's for the same reason people have been playing and modding games like these (Doom, Quake, Thief, Jagged Alliance, X-COM etc) for years, not only because they are modable, but also because their foundation is so good.