Get the Flowmasters. They are actually pretty damn good as far as quality goes. I had their American Thunder kit on my old '91 GT. I also used those mufflers with a set of their polished stainless steel pipes on my '90 LX. There was absolutely nothing wrong with the quality, in fact, I was actually impressed with the stainless pipes. And they still look good today.
Flow-through mufflers make a little more power (and when I say little, I mean little... as in 1-2), but don't purchase a muffler based on how much power it will "make". Get the mufflers you think sound best.
In my opinion, Flowmasters are the best sound mufflers you can buy. To me, straight-through mufflers sound like ass. They are bad about popping and the sound reminds me more of Civics than a good ol' hunk of American iron.