In that regard we play the same. I usually have my capital pegged as the science city. To keep its GPP from being "polluted", I prefer to not build Great Prophet-generating wonders there, such as Stonehenge and the Oracle. So I almost always build them in my second city instead. That means the 2nd city has to have a decent production resource in its first ring, however.
If the map doesn't lend itself to this, I'll do a switcheroo--build Stonehenge and the Oracle in the capital and select a different city for science.
right but that does mean that before building stonehenge I:
- built a warrior
- built a worker
- built a settler
- sent the settler to a settle in a nice production spot (preferably with copper)
That's enough to build stonehenge in the capital, if you start with mysticism.
And it's also enough to :
- research masonry
- research wheel
- connect stone