It depends on the style of beer, but I'd go with the shorter time in the primary. It will be better for the beer to leave it in the bottles longer. It can stay in the bottles for a while but you generally do not want beer in the primary for any longer than 4 weeks. While it's not necessarily a bad thing, less contact with the trub will produce a better beer. The other alternative you could do is, 1-2 weeks primary, 2 weeks secondary, and then 2+ weeks in bottles. There are mixed views about secondary fermentation but it does help clarify the beer.
-Jeff