Secondary Fermentor vs. Bottle Conditioning
Conditioning is a function of the yeast, therefore it is logical that the greater yeast mass in the fermentor is more effective at conditioning than the smaller amount of suspended yeast in the bottle. This is why I recommend that you give your beer more time in the fermentor before bottling. When you add the priming sugar and bottle your beer, the yeast go through the same three stages of fermentation as the main batch, including the production of byproducts. If the beer is bottled early, i.e. 1 week old, then that small amount of yeast in the bottle has to do the double task of conditioning the priming byproducts as well as those from the main ferment. You could very well end up with an off-flavored batch.
Do not be confused, I am not saying that bottle conditioning is bad, it is different. Studies have shown that priming and bottle conditioning is a very unique form of fermentation due to the oxygen present in the head space of the bottle. Additional fermentables have been added to the beer to produce the carbonation, and this results in very different ester profiles than those that are normally produced in the main fermentor. In some styles, like Belgian Strong Ale, bottle conditioning and the resultant flavors are the hallmark of the style. These styles cannot be produced with the same flavors via kegging.
For the best results, the beer should be given time in a secondary fermentor before priming and bottling. Even if the yeast have flocculated and the beer has cleared, there are still active yeast in suspension that will ferment the priming sugar and carbonate the beer.