I will throw this in for your consideration, debate, and scorn:
Plastic comparison
DX v Pro D - DX just seems harder and more damage resistant which is a plus in all discs besides a few putters that may fly better with Pro D style damage.
Pro v Elite X - Pros just seem faster while Xs seem to have better glide than their comparable molds in other plastics. This is nearly a toss up, but I like how the Pro feels more so than the X.
Champion v Elite Z - Champions have richer color but Z I think overall have better color selection. I think Z grips a little better and is more durable than Champion.
Star v ESP - I find Star far more durable than ESP with exceptions like the ESP Pulse, which is nearly indestructible for some reason. I also like the grip of Star considerably more than ESP. However, at least in mids, ESP seems to have more glide than Star.
Non-comparible plastics - Innova has the R-Pro and Echo Star while Discraft has FLX. For what they are intended I think Innova has this category due to the Echo Star. That particular plastic is a great compromise between Star and Pro. For the most part FLX's job of being durable far outweighs R-Pro's job of being grippy. Otherwise, it really is hard to compare discs in these plastics unless you look just at what they are intended to do.
Innova Putters v Discraft Putters - I give this category to Discraft because of how many operable putters they have. Innova may have the several versions of Aviars, but the same is true of Magnets. Discraft just has more of a selection.
Innova Midrange v Discraft Midrange - I give Discraft another nod and mainly again to selection. They have the Buzzz, the Buzzz SS, Meteor, Wasp, Hornet, and Drone. This is quite a formniable lineup. While the Roc is definitely no slouch, at best it can be paired with a Mako and Shark. Innova obviously has other mids, but I think Discraft just has a higher average quality of mids.
Innova Drivers v Discraft Drivers - To keep this short I lumped Fairway and Distance drivers together. Innova has a huge advantage in Fairways; Teebirds, TLs, Leopards, and so on comparable to Discraft's big two of Cyclones and Stalkers. XS and XL are definitely nice discs, do not get me wrong, but their inconsistencies between plastics is far greater than the inconsistencies between those in Innova's lineup. I think Discraft's Nuke lineup definitely brings them back into the driver conversation as Innova can only answer with the Boss, Katana, and Ape, but if you throw in there the XCaliber, Wraith, Orc, TeeDevil, Valkyrie, and Destroyer, they cover far more stability ground than the Crush, Force, Surge, and Surge SS.
Basically both companies are great, and unless you are a sponsored player who has spent a great deal of time learning specific discs and breaking them in to your ideal stability and style, a mixed bag definitely seems best.