What are you planning to use it for? If you are going to be waterfowling, then the 3.5" may be a consideration, however many people chose not to use 3.5" foe various reasons. If you are just using it for clays or grouse, there is no need to be able to have ability to use 3.5" shells, however the system in my SX2 handles anything you feed it from the lightest 2 3/4 target load to 3.5" without a hitch.
When I was looking for my SX2, I looked at it like horsepower in a truck. You may not always need the capability of a 6L V8, but when you do it's there. Same goes for the 3.5" shells. I only occasionally use them, but when the geese are staying further out, or the ducks aren't decoying well, I can drop a shot size and keep the same pellet count by moving up to a 3.5" shell.
Just my $0.02