secondary vs bottle won't matter too much. Both have the bulk of yeast removed. In some cases, you want to keep it on the yeast to clean up fermentation byproducts - especially with bigger beers and lagers.
Past that, no big deal. GiB make a good point about dry hopping, though. If you bulk age in secondary, you can always add dry hops just before bottling. However, there's no greater chance to infection if it's left in secondary. If your fermentor isn't clean and sanitized in the first place, it doesn't matter how long you keep the beer in there.