If you plan to keep the car and run more boost (better tune) I'd go the whole way with 3", find a different shop that thinks they can do it.

I've been running a z6 on 2.5" for a few years now, already wish I would have gone with 3", but I'm running 13psi on a .60/.48 and want to go bigger.

If the car is a daily I'd go the 2.5 route w/ muffler, and a resonator on the long stretch of 3".