There are pros and cons to each approach. In most cases, a long primary will be better than using a secondary fermentation vessel.
There are three distinct advantages to leaving the beer in primary, without using a secondary at all:
- There is less risk of oxidation and infection since one transfer is eliminated.
- You do not need an expensive carboy to use as a secondary.
- It's less trouble.
There are also several disadvantages of performing a long primary fermentation:
- If you are using plastic buckets, a very long primary (more than 4 weeks) will allow some oxygen to contact the beer. The plastic that the fermentation buckets are made of is slightly oxygen-permeable.
- Since oxidation is not a concern, a longer aging in a glass container can produce a beer with greater clarity. This may also be possible with a primary performed in a glass carboy, except:
- A long primary may lead to autolysis (yeast death, after which their guts spill into your brew.) The common consensus seems to be that autolysis flavors will only manifest after extremely long times in primary. Perhaps three months or more.
There are a few cases where a secondary vessel is advantageous:
- You will need one if you are adding fruit to the beer. This is usually done by racking the beer on top of a pile of fruit or fruit puree in the secondary fermenter.
- Some brewers prefer to dry-hop in a secondary fermenter (this can also be accomplished in a keg)