A lot of people like the magnaflow sound with the matched resonator, and instead of 2.5" to the Y and then 2" to the muffler you get 2.5" the whole way. Plus it bolts on easy and looks really clean, and you get measurable HP gains. As far as bolt on mods go, I've never heard anyone complain after they bought one.
That said, I saw an article by a Dynomax engineer that claimed there is only 2-4 HP to be found in the piping if you keep the same size or make a small increase. Now if you were making a lot more HP than stock, or had a power adder, then the exhaust pipe size will become a restriction and rob more power, but for a mostly stock car there isn't much power there.
You DO take a big hit in the cat and the mufflers. You can buy most aftermarket mufflers for about $70 each in a 2.25" size, and a Hogan downpipe with a high-flow cat is $300. Throw in a trip to your exhaust shop to get the mufflers welded on, res delete, and maybe some tips, and I think you get more bang for your buck. But since there are so few bolt-ons for this engine and every HP counts, I think the Magnaflow kit will max out your performance even if it costs more.
Personally, I'm eyeballing a set of Hooker Maxflows (quiet at idle and cruise, really loud at WOT, nice power gains) if they fit (I haven't measured yet), but Magnaflows are my second choice. I like glasspacks over chambered mufflers, but a lot of guys love that flowmaster sound too.
BTW, I heard there are ways to get the kit cheaper than $698 just by shopping around and asking. The cheapest I've read is $516 shipped, but I don't have any personal experience.