The PS2 version is better.
You already said the reason; it's darker.
Dark and gritty is the charm of Liberty City (in both 3D and HD era).
Liberty City was all shiny and colorful back in the first GTA and GTA Advance, and their Liberty Cities wasn't so interesting at all.
PS: And also, PS2 version has a a better resolution (480i/576i), better draw distance and better textures...But this is coming from a graphics whore like me.