Well, actually, Liu Kang was more the Ryu, and there was no Ken at that point(maybe Kung Lao? Johnny Cage? Obviously Sonya is the Chun-Li).
Though yeah, nowadays they're the Ryu and Ken. It just wasn't their actual roles till Liu Kang got massacred(in-universe and out-of-universe). I think Scorpion might have higher priority, so Sub-Zero being the echo makes sense. Though to be fair, my main argument against the echo idea was that the Klassic versions weren't that likely to be used. I was beyond wrong on Ed Boon's opinion on that, so I have no real argument for why it couldn't happen. Especially since only having one in would be very unpopular. It's not like with Ken, who doesn't have to be in while Ryu is in. They're not on equal grounds by any means when it comes to popularity. Scorpion and Sub-Zero are a very different story. When Scorpion or Sub-Zero weren't in an MK game, it had a lot of backlash. UMK3 was created just to fix this issue alone.
Pretty much. I don't think it'd be a problem with animations, as they'd just need new ones. Though the 3D games changed it up more, the 2D games were famous for every MK character having the same normals to some degree. Scorpion and Sub-Zero being clones(for many moves besides the basic ones) also helped, as they had nearly identical combos due to being palette swaps and all.
That said, figuring out a good costume list is difficult. Assuming Scorpion wouldn't get colors based upon the Sub-Zero duo, that is. Plus, Sub-Zero has his Shredder helmet, which helps differentiate him. Though perhaps they could go more with their Modern looks, but use their Klassic abilities/bodyshapes.