While I didn't buy this game, as I saw the eventual trainwreck coming months before it was released, I feel making the engine "track the entire population simultaneously" was an ambitious and admirable goal, but ultimately, a naive and fatal decision. The sheer amount of computation required to model 100,000 individual "agents" realistically moving and interacting in a city or multiple cities is immense. I don't think making traffic patterns much more realistic is a trivial fix here. And if Maxis were able to do so with the current engine, then I believe the minimum RAM requirement would significantly jump.
And then to scale that up to much larger sized cities... ...I'm not sure if anyone here would have a PC to run that game... I don't think Maxis has a PC to make/test that game. I doubt modders are going to make the difference some people here think they will.
Basically, if you want a SimCity 4-like city simulator, I think Maxis and EA are going to have to scrap the current engine and start from square one. To me, I'd focus on regional transportation systems (networks of highways of varying sizes, light rail, heavy rail, etc.) as the big, new improved feature over SimCity 4 and model cities' populi more akin to SimCity 4 than SimSuburb.