Agreed that if businesses aren't properly spread out, then rush hour traffic will always be bad. What else can you expect if your city effectively shrinks to 1/10th its size every day at 9 AM and 6 PM?
I live just outside the center (to the north, Ouji-Kamiya), and my workplace is just outside the city center (to the south, Naka-meguro), and it takes me about an hour door-to-door to cut across the city (50 minutes station to station), with 2 transits.
This is probably the longest possible way to cut across the city in public transportation, but I think you can expect 45 minutes to cut across in general, given transits.
The other problem is that the center is less than 15 miles in diameter, so a bit hard to get the same "feel" as LA for the comparison.