Imo every difference resides in the new scripting lua language (used from shogun 2 if I'm correct).
I'm not a scripter (the only experience I have with scripting is through M2TW and Rome2) but lua it is far more complex and has a lot of possibilities (se what Litharion did for population or prime for people's trust).
With M2TW you could never had deep scripted systems (that can go outside normal game mechanics)
Sincerely I don't think that anyone can really say that M2TW (and mods) are better than Rome2's in any feature (well maybe just a couple, but almost secondary features).
Think it is just the nostalgic part speaking (and the fact that maps were moddable and people could "create" a world)