'advanced' is subjective. vanilla doom3 doesn't support glsl, while fte+dp both (ab)use it as much as they can, so in terms of renderer features, yeah, the '96 derivatives win...
but there's two things not available to the q1 derivatives, and that is ragdoll and code to invoke that ragdoll (thus tying the entire world into a single cohesive physics system). I really cannot express how important that is for a modern FPS.
Yeah, you can create ODE objects, but frankly I still personally only see that as a gimmick feature rather than something you can base a full game upon. Both engines are capable of drawing skeletal objects in pretty much any pose, but there's no code that actually uses it and thus its pretty much useless to the average person around here.
an engine is nothing without a purpose, and doom3's is much more focused upon that purpose, thus what is there is much more useful.
that said, doom3 has a max player limit of 4 or something stupid... which is more of a joke than a real attempt. so yeah, its all subjective.

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