I used to do that too since I got most of my gold from commerce (using the %gold slider setting) and I also got most of my science from commerce (using the %science slider setting). With Bureaucracy pushing your commerce up by 50%, it was pretty obvious to put those two in my capital.
...especially since my capital usually had a couple of good food resources and lots and lots of towns.
As I've played the game more and more, I've seen that I get a lot more effectiveness out of pulling most of my empire's gold needs from one city and leaving my science slider as high as I possibly can. That means I'm getting most of my gold from a religious shrine, settled Great Priests (I don't usually settle Great Merchants) and from corporations late in the game. That one city can produce such a rediculous amount of gold that I can get all of my empire's needs from that city, so Wall Street goes there. Amusingly, I find that is often a neighbor's Buddhism/Hinduism shrine, so I do end up putting Oxford and Wall Street both in the Capital. It's just that Oxford is my capital while the Wall Street city is someone else's former capital instead of my current one.
The biggest reason why I find this effective is that I like to use the larger maps, so getting an extra +100% on the 1

per city that has the religion is a lot more substantial than the gold I would get from even a great cottage/town city.
Other combinations that I find very effective are Heroic Epic + Settled Great Generals and NO OTHER NATIONAL WONDER. Once I build Heroic Epic, that production boost to units is so important that I can't afford to "waste" hammers building things that aren't units in that city.
Japan can get power from Shale Plants without Coal, so a Shale Plant with your factory in the National Park city makes an absolutely amazing production powerhouse because it still gets the +50% production bonus for power (which most empires' National Park cities will never see because National Park keeps coal out of that city as a side effect from the wonder). This is actually such a good production city that I'll even put the Iron Works in the National Park city for Japan sometimes. (The extra Engineer slots make this worthwhile for me.)
I never put the National Epic in the same city as the National Park even though it is such an obvious combination. That's because I have the National Epic complete in some other high food city centuries before my National Park city will even be possible.