Think of this nearly the exact same way, except it's actually "all the possibilities of CoD's create a class x 40", since COD doesn't have a few dozen characters. 40 is just a ballpark number, to be clear, and I'm sure it's on the low end of what we can expect over the game's lifespan. The exact value doesn't really matter; my point is it amounts to "(a) characters x (b) possibilities", where (a) represents a shitload and (b) represents another shitload.
Yeah, it's a cool concept to think about, until you realize that more possibilities = more balance issues. Always. This doesn't necessarily mean a game with more options is going to be less balanced than a game with fewer options, but it will be harder to balance. Be amazed that MKX is as good a game as it is, because with 3 variations for each character to account for (and 4 for that extra special someone), NRS had their work cut out for them. This poll is the same general idea, except it's a game with more characters, and you're essentially letting people build their own variations from all the options available. Anyone who has ever felt frustrated with MKX's balance (I said it's good, not perfect) can probably try to imagine a world in which MKX not only allows you to mix and match all of the variation differences, but also has a bigger roster to further complicate the issue.
I don't think I need to paint you a picture, here.
Now, the one thing the devs COULD do (and I still find this unlikely) is implement presets for each character. If each character had two presets with alternate gear/movelists, that's more or less the equivalent of MKX's three variations. I always wondered why Smash 4 didn't take this route, because the general consensus seems to be that some of the worst characters are made significantly better by swapping out specials. If anything like this did happen with IGAU, I would assume it'd be later in the game's lifespan, around the time it gets the MKXL treatment, because this late in a game's dev cycle, it's pretty much "done". NRS could also implement this very easily, but that doesn't mean they will. MKX's variation system was a great idea, but again, it obviously makes balancing the game much more difficult. This would be no different. If NRS just doesn't want to bother with all that added complication, I can't blame them. Regardless, that seems like the only way an idea like this could ever see the light of day.