I think the new Subway changes are great. Small touches like wandering mobs give the whole place a more active, and much less boring atmosphere.
And this is off-topic, but I'm sure we've all noticed how FC likes to put random literary references in the game. There's Vergil Aeneid, the next subway boss after Eumenides, which references Vergil's book, The Aeneid. In 10-3 there's a robot named "Marvin the Paranoid Android" which is a reference to the Hitchhikers Guide to the Galaxy.
I'm sure there's more that I'm forgetting or don't know about.