I think most of it is personal preference. The same reason I choose Addidas over Nike (other than growing up, I could wear them for several years where Nike wore out in 1).
The way I came about being more of a Discraft person was from when I started. I was out on the course with one disc, and some Discraft sponsored people would let me try their stuff and often keep one or two of them. I have a cyclone, cyclone 2, magnet, mrx (or is it mrv, I get them confused), xs, and xl that were given to me. At the time, Innova was easier to get at Academys, but I would be buying a disc without trying it. It wasn't the free stuff that was most important, but the, "here try this," attitude that the Discraft guys have.
I'm not sure that they were sponsored, but the Innova guys did just the opposite. I felt like a kid getting griped at by his parents for throwing Discraft. I was using an old backpack at the time, and they liked going through my stuff to complain about it, which I have never understood.
I currently am more of a Discraft person though I throw the wraith and demon & wizard from Gateway. I try out all the Innova discs that come out, yet I don't find them to be THAT much better (if better at all) than their Discraft equivalents: wraith being the exception and maybe the stingray.