If you have the choice, go for a 3" job. It's not only the extra power it may release but, it will also improve spool up and torque.
Plus, you'll wish you had gone for a bigger system later on, if you only go for the 2.5" job !
A 3" system doesn't have to be louder either. My view is that if it's designed well, and the right parts (silencers) are used, it can be as quiet and as free flowing as you want it to be.
