A few reasons to go to a 3" system:
1. You are planning on exceeding 600-650 bhp (the generally recognized ceiling for a 2.5" system)
2. You are going to use or are using Forced Induction
3. You want a deeper exhaust tone with no rasp
A few reasons NOT to go to a 3" system:
1. In and of itself, a 3" system won't net you much in the way of HP unless you are very heavily modded.
1a. Requires a change to headers to really take advantage of the 3" system
2. Depending on the material/design of the 3" system you can actually ADD weight to the car.
3. Makes accessing the diff drain plug (among other things) very difficult
4. Some systems are difficult to get/keep aligned and require you to shim the stock tunnel brace for clearance or replace it
These are my experiences with my car along my modification path, YRMV. Others will chime in with their thoughts I'm sure...