I have a Yamaha XJ6 from 2012 and I would like to change the exhaust. But I have a choice.
Do I change only the muffler or the whole "line"?
Other than cost what are the pros and cons of changing the muffler vs. the whole line?
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The 2012 XJ6 is fuel injected, so an aftermarket exhaust (Arrows, Leo Vince, Scorpion, Two Brothers, Akrapovic etc) would be easily procured. You may even get good deals on used slip-on exhausts, and you could then re-pack the glass wool (other as applicable) if required.
In order to keep the cost down, you could opt for a slip-on exhaust (muffler) instead of a full-system ("whole line"). In either case, some performance benefits and varying levels of exhaust note changes will be obtained. In either case, significant weight reduction is possible. In my case, the stock exhaust was 11 kilos, while my aftermarket full system was under 3.5 kilos.
The stock maps that come tuned for the stock exhaust may not allow you to extract all that the aftermarket exhaust could give. For this, a piggy-back module like the Dynojet Power Commander, or Bazzaz units that allow you to load a different (read richer) map will help with the gain in performance you would desire. In addition, such units allow you to get rid of flat spots in the stock map, to keep the power delivery linear over the rev-range.
There are other options like Tuneboy and Flashtune that remap the stock ECU instead of requiring a piggy-back unit. However, these may void your warranty.
Please be aware that certain cities have regulations that govern the permitted sound level for exhausts. Most exhausts come with baffles that reduce the sound output to an extent. Please check the regulations in your area of use before you pull the trigger.