more air in / more exhaust out = better for performance. Many people dyno'ed higher numbers with 3" exhausts on the 8th gen civics versus 2.75" or whatever on the SI. That's why you'll see numerous companies selling 3" exhausts for the 9th gen.
I mean how in depth of an answer do you want? Overall, the larger the exhaust the better the gains have been for the Civic. Especially if you are considering going turbo or supercharger route later, the 3" exhaust is the way to go. Generally no cons to any larger exhaust than noise increase and more $$ but not necessarily.
If you're concerned for noise, the Invidia Q300 has been one of the quietest exhausts will good gains. It's so quiet some people have switched since they felt it wasn't loud enough over the stock system.
Thanks Nix and Webby. There are soooo many conflicting reports that you lose low end power with the 2.5. I can't tell who is correct. I am not going turbo, just basic exhaust CAI and maybe headers.