Having fought with my UPR X-pipe for some time now, I'd definitely recommend the Magnaflow. For one, the cats on the Magnaflow are farther back to allow for more clearance, whereas the UPR X has them right where the tranny crossmember humps are, and (on mine) I had to notch out 1" of material from the crossmember just to make the whole deal fit without leaking at the header flange from being at a weird angle. (If they had placed them just an inch or so forward, or closer to the X-over, it wouldn't have been an issue.)
Another issue is that the UPR unit has a two-piece design, by which you have to hang one side, then fiddle around to hang the other, and somehow find a comfortable compromise between where one side wants to sit versus the other. My passenger's side pipe has tons of free room but, as stated, my driver's side cat was (and still is) woefully crammed right up against the crossmember. I literally could not make the thing fit on there AT ALL if I hadn't notched the crossmember, short of pounding a big indentation into the casing of the cat to make it clear. The lack of having to mess with those two stupid hangers in the middle (the two secured at the tranny mount) was a nice bonus, as well as not having to deal with hooking up an A.I.R. tube from the smog pump to the cats (the UPR setup doesn't use the smog pump tube at all), but otherwise ... ugh. Wish to heck I didn't have to have cats at all in my area, or I'd have just gotten the off-road version and been done with it.
As it is now, it still gets a thump here and there against the crossmember, and ground clearance is only about 1" (if even that much) better than the crappy Frankenstein'ed-together H-pipe that it replaced. It does, however, sound VERY nice at WOT, and there is a noticeable gain over the crappy setup I had before.
In hindsight, I wish I'd just spent the extra bucks and gone with the Magnaflow X, or even a plain ol' Catco brand H-pipe, instead of all the crap I had to go through just to make the UPR setup work.