depends what you want. louder or a more mellow refined sound? flowmaster is louder, magnaflow is quieter. I personally have flowmasters with the resonator removed and love it. people complain about drone when driving but personally it doesnt bother me and isn't something the radio cant hide. some people are super anal about it the sound though and don't like that
I put a brand new flowmaster on my jeep and it rusted out 6 months lster. Keep in mind i live in cali and its always sunny and warm. No reason for it to do that. Put another and the weld on the muffler seam came undone. Magnaflow is just awesome. Better materials etc, put one on my 64 and it sounds awesome and its a nice stainless one
A buddy of mine put a 70 series flowmaster on his monte carlo several years ago, within a couple years one of the baffles broke loose and came out the tailpipe. So I would say that combined with everyone else's stories, they probably have a few quality control issues...
I've had good luck with Flowmasters many times over the years without any quality issues.
That said, I would recommend the Magnaflow style muffler for your 3.6L. Chambered mufflers (like Flowmasters) tend to sound great on V8s, but V6s tend to sound like crap with them - whether it's due to the firing order/exhaust pulses or just the lower volume of exhaust, I don't know.
Magnaflows are more traditional fiberglass packed style mufflers and would probably sound awesome with your 3.6L.